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Protein

Genome polyprotein

Gene
N/A
Organism
Poliovirus type 1 (strain Mahoney)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Capsid protein VP1: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Capsid protein VP1 mainly forms the vertices of the capsid. Capsid protein VP1 interacts with host cell receptor PVR to provide virion attachment to target host epithelial cells. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. Tyrosine kinases are probably involved in the entry process. Virus binding to PVR induces increased junctional permeability and rearrangement of junctional proteins. Modulation of endothelial tight junctions, as well as cytolytic infection of endothelial cells themselves, may result in loss of endothelial integrity which may help the virus to reach the CNS. After binding to its receptor, the capsid undergoes conformational changes. Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized. Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm. After genome has been released, the channel shrinks.
Capsid protein VP2: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome.
Capsid protein VP3: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome.
Capsid protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm. After genome has been released, the channel shrinks (By similarity).By similarity
Capsid protein VP0: Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step (By similarity).By similarity
Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores including NUP98, NUP62 and NUP153.
Protein 2B: Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication.
Protein 2C: Induces and associates with structural rearrangements of intracellular membranes. Triggers host autophagy by interacting with host BECN1 and thereby promotes viral replication. Participates in viral replication and interacts with host DHX9. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.
Protein 3AB: Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity.
Protein 3A: Localizes the viral replication complex to the surface of membranous vesicles. It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the dissassembly of the Golgi complex, possibly through GBF1 interaction. This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface.
Viral protein genome-linked: acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU. The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication.
Protein 3CD: Is involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD lacks polymerase activity. The 3C domain in the context of protein 3CD may have an RNA binding activity.
Protease 3C: May cleave host PABP and contribute to host translation shutoff.
RNA-directed RNA polymerase: Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss+RNA genomes are either translated, replicated or encapsidated.

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein.
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
NTP + H2O = NDP + phosphate.

Enzyme regulationi

RNA-directed RNA polymerase: replication or transcription is subject to high level of random mutations by the nucleotide analog ribavirin.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei25Involved in the interaction with human RTN3By similarity1
Active sitei901For Protease 2A activityBy similarity1
Active sitei919For Protease 2A activityBy similarity1
Active sitei990For Protease 2A activityBy similarity1
Active sitei1605For Protease 3C activitySequence analysis1
Active sitei1636For Protease 3C activitySequence analysis1
Active sitei1712For Protease 3C activitySequence analysis1
Active sitei2076For RdRp activity1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1256 – 1263ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Ion channel, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase, Viral ion channel

Keywords - Biological processi

Activation of host autophagy by virus, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host mRNA suppression by virus, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host mRNA nuclear export by virus, Inhibition of host RIG-I by virus, Inhibition of host RLR pathway by virus, Ion transport, Pore-mediated penetration of viral genome into host cell, Transport, Viral attachment to host cell, Viral immunoevasion, Viral penetration into host cytoplasm, Viral RNA replication, Virus endocytosis by host, Virus entry into host cell

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Protein family/group databases

MEROPSiN08.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 17 chains:
Alternative name(s):
VP4-VP2
Alternative name(s):
P1A
Virion protein 4
Alternative name(s):
P1B
Virion protein 2
Alternative name(s):
P1C
Virion protein 3
Alternative name(s):
P1D
Virion protein 1
Protease 2A (EC:3.4.22.29)
Short name:
P2A
Alternative name(s):
Picornain 2A
Protein 2A
Protein 2B
Short name:
P2B
Protein 2C (EC:3.6.1.15)
Short name:
P2C
Protein 3A
Short name:
P3A
Alternative name(s):
Protein 3B
Short name:
P3B
Protease 3C (EC:3.4.22.28)
Short name:
P3C
Alternative name(s):
3D polymerase
Short name:
3Dpol
Protein 3D
Short name:
3D
OrganismiPoliovirus type 1 (strain Mahoney)
Taxonomic identifieri12081 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeEnterovirusEnterovirus C
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000000356 Componenti: Genome

Subcellular locationi

Protein 2B :
Protein 2C :
Protein 3A :
Protein 3AB :
Protein 3CD :
RNA-directed RNA polymerase :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini2 – 1520CytoplasmicSequence analysisAdd BLAST1519
Intramembranei1521 – 1536Sequence analysisAdd BLAST16
Topological domaini1537 – 2209CytoplasmicSequence analysisAdd BLAST673

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Host cytoplasmic vesicle, Host membrane, Membrane, T=pseudo3 icosahedral capsid protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi2G → A: 100% loss of myristoylation. Impaired viral assembly. 1 Publication1
Mutagenesisi3A → D: 50% loss of myristoylation. Severe reduction in specific infectivity. 1 Publication1
Mutagenesisi3A → G, L or V: No effect on myristoylation and virus growth. 1 Publication1
Mutagenesisi3A → H: No effect on myristoylation. Severe reduction in specific infectivity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL5127.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostBy similarity
ChainiPRO_00004246862 – 2209Genome polyproteinAdd BLAST2208
ChainiPRO_00004246872 – 881P1Add BLAST880
ChainiPRO_00004246882 – 341Capsid protein VP0Sequence analysisAdd BLAST340
ChainiPRO_00000400802 – 69Capsid protein VP4Sequence analysisAdd BLAST68
ChainiPRO_000004008170 – 341Capsid protein VP2Sequence analysisAdd BLAST272
ChainiPRO_0000040082342 – 579Capsid protein VP3Sequence analysisAdd BLAST238
ChainiPRO_0000040083580 – 881Capsid protein VP1Sequence analysisAdd BLAST302
ChainiPRO_0000424689882 – 1456P2Add BLAST575
ChainiPRO_0000040084882 – 1030Protease 2ASequence analysisAdd BLAST149
ChainiPRO_00000400851031 – 1127Protein 2BSequence analysisAdd BLAST97
ChainiPRO_00000400861128 – 1456Protein 2CSequence analysisAdd BLAST329
ChainiPRO_00004246901457 – 2209P3Add BLAST753
ChainiPRO_00004246911457 – 1565Protein 3ABSequence analysisAdd BLAST109
ChainiPRO_00004246921457 – 1543Protein 3ASequence analysisAdd BLAST87
ChainiPRO_00000400881544 – 1565Viral protein genome-linkedSequence analysisAdd BLAST22
ChainiPRO_00004246931566 – 2209Protein 3CDSequence analysisAdd BLAST644
ChainiPRO_00000400891566 – 1747Protease 3CSequence analysisAdd BLAST182
ChainiPRO_00000400901748 – 2209RNA-directed RNA polymeraseAdd BLAST462

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by host3 Publications1
Modified residuei1546O-(5'-phospho-RNA)-tyrosine1
Modified residuei1546O-UMP-tyrosine; transient2 Publications1

Post-translational modificationi

Capsid protein VP0: Myristoylation is required for the formation of pentamers during virus assembly. Further assembly of 12 pentamers and a molecule of genomic RNA generates the provirion (By similarity).By similarity
Genome polyprotein: Specific enzymatic cleavages in vivo by the viral proteases yield processing intermediates and the mature proteins.
Capsid protein VP0: During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and it is followed by a conformational change infectious virion.
Viral protein genome-linked: VPg is uridylylated by the polymerase into VPg-pUpU. This acts as a nucleotide-peptide primer for the genomic RNA replication.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei69 – 70Cleavage; by autolysisSequence analysis2
Sitei341 – 342Cleavage; by Protease 3CSequence analysis2
Sitei881 – 882Cleavage; by Protease 2ASequence analysis2
Sitei1030 – 1031Cleavage; by Protease 3CSequence analysis2
Sitei1127 – 1128Cleavage; by Protease 3CSequence analysis2
Sitei1456 – 1457Cleavage; by Protease 3CSequence analysis2
Sitei1543 – 1544Cleavage; by Protease 3CSequence analysis2
Sitei1565 – 1566Cleavage; by Protease 3CSequence analysis2
Sitei1748 – 1749Cleavage; by Protease 3CSequence analysis2

Keywords - PTMi

Covalent protein-RNA linkage, Lipoprotein, Myristate, Phosphoprotein

Miscellaneous databases

PMAP-CutDBP03299.

Interactioni

Subunit structurei

Capsid protein VP1: Interacts with capsid protein VP0, and capsid protein VP3 to form heterotrimeric protomers. Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid. Interacts with human PVR. Interacts with capsid protein VP4 in the mature capsid. Capsid protein VP0: interacts with capsid protein VP1 and capsid protein VP3 to form heterotrimeric protomers. Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid. Capsid protein VP2: Interacts with capsid protein VP1 and capsid protein VP3 in the mature capsid. Capsid protein VP3: interacts with capsid protein VP0 and capsid protein VP1 to form heterotrimeric protomers. Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid. Interacts with capsid protein VP4 in the mature capsid. Capsid protein VP4: Interacts with capsid protein VP1 and capsid protein VP3. Protein 2C: interacts with cellular Vimentin/VIM and BECN1; these interactions play important roles in the viral replication (By similarity). Protein 2C: interacts with capsid protein VP3; this interaction may be important for virion morphogenesis. Protein 2C: interacts with host BECN1 and DHX9 and possibly presents a hexameric ring structure with 6-fold symmetry characteristic of AAA+ ATPases. Protein 2C: N-terminus interacts with human RTN3. This interaction is important for viral replication (By similarity). Protein 3AB: interacts with protein 3CD. Protein 3A: homodimerizes and interacts with host GBF1. Viral protein genome-linked: interacts with RNA-directed RNA polymerase. Protein 3CD: interacts with protein 3AB and with RNA-directed RNA polymerase. RNA-directed RNA polymerase: interacts with Viral protein genome-linked and with protein 3CD.By similarity7 Publications

Chemistry databases

BindingDBiP03300.

Structurei

Secondary structure

12209
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 7Combined sources5
Beta strandi17 – 23Combined sources7
Beta strandi26 – 29Combined sources4
Beta strandi33 – 35Combined sources3
Helixi36 – 38Combined sources3
Helixi51 – 54Combined sources4
Beta strandi57 – 59Combined sources3
Helixi66 – 69Combined sources4
Helixi74 – 76Combined sources3
Beta strandi83 – 87Combined sources5
Beta strandi90 – 96Combined sources7
Beta strandi100 – 102Combined sources3
Helixi103 – 105Combined sources3
Helixi113 – 115Combined sources3
Helixi126 – 128Combined sources3
Beta strandi138 – 141Combined sources4
Beta strandi147 – 151Combined sources5
Helixi153 – 155Combined sources3
Helixi159 – 167Combined sources9
Beta strandi168 – 180Combined sources13
Beta strandi187 – 197Combined sources11
Beta strandi206 – 210Combined sources5
Helixi214 – 217Combined sources4
Helixi220 – 222Combined sources3
Beta strandi227 – 229Combined sources3
Beta strandi236 – 238Combined sources3
Helixi247 – 249Combined sources3
Turni250 – 253Combined sources4
Helixi256 – 261Combined sources6
Beta strandi262 – 268Combined sources7
Turni269 – 271Combined sources3
Beta strandi273 – 279Combined sources7
Beta strandi284 – 288Combined sources5
Turni290 – 292Combined sources3
Beta strandi296 – 308Combined sources13
Beta strandi311 – 313Combined sources3
Beta strandi315 – 332Combined sources18
Turni349 – 352Combined sources4
Beta strandi364 – 366Combined sources3
Beta strandi380 – 383Combined sources4
Helixi384 – 388Combined sources5
Turni400 – 404Combined sources5
Helixi406 – 409Combined sources4
Beta strandi411 – 414Combined sources4
Beta strandi423 – 428Combined sources6
Turni430 – 432Combined sources3
Turni434 – 438Combined sources5
Helixi440 – 445Combined sources6
Beta strandi448 – 453Combined sources6
Beta strandi455 – 461Combined sources7
Beta strandi470 – 476Combined sources7
Beta strandi478 – 480Combined sources3
Helixi486 – 489Combined sources4
Beta strandi492 – 498Combined sources7
Beta strandi500 – 502Combined sources3
Beta strandi504 – 509Combined sources6
Beta strandi514 – 521Combined sources8
Helixi524 – 526Combined sources3
Beta strandi530 – 537Combined sources8
Beta strandi547 – 557Combined sources11
Beta strandi562 – 566Combined sources5
Beta strandi570 – 572Combined sources3
Beta strandi586 – 589Combined sources4
Beta strandi594 – 596Combined sources3
Helixi626 – 628Combined sources3
Helixi636 – 638Combined sources3
Helixi652 – 654Combined sources3
Helixi656 – 660Combined sources5
Beta strandi664 – 673Combined sources10
Beta strandi685 – 688Combined sources4
Beta strandi693 – 695Combined sources3
Helixi696 – 701Combined sources6
Beta strandi704 – 721Combined sources18
Beta strandi723 – 725Combined sources3
Beta strandi733 – 739Combined sources7
Helixi752 – 755Combined sources4
Beta strandi757 – 759Combined sources3
Beta strandi761 – 765Combined sources5
Beta strandi771 – 775Combined sources5
Beta strandi780 – 786Combined sources7
Beta strandi790 – 793Combined sources4
Beta strandi796 – 799Combined sources4
Turni801 – 804Combined sources4
Helixi812 – 814Combined sources3
Beta strandi818 – 823Combined sources6
Beta strandi832 – 850Combined sources19
Beta strandi860 – 863Combined sources4
Helixi1478 – 1484Combined sources7
Helixi1487 – 1496Combined sources10
Beta strandi1546 – 1550Combined sources5
Beta strandi1556 – 1558Combined sources3
Helixi1560 – 1564Combined sources5
Helixi1567 – 1579Combined sources13
Beta strandi1580 – 1585Combined sources6
Beta strandi1588 – 1597Combined sources10
Beta strandi1599 – 1603Combined sources5
Helixi1604 – 1606Combined sources3
Beta strandi1610 – 1614Combined sources5
Beta strandi1617 – 1628Combined sources12
Beta strandi1634 – 1645Combined sources12
Helixi1652 – 1654Combined sources3
Beta strandi1662 – 1669Combined sources8
Beta strandi1671 – 1674Combined sources4
Beta strandi1677 – 1692Combined sources16
Beta strandi1695 – 1705Combined sources11
Beta strandi1715 – 1718Combined sources4
Beta strandi1721 – 1729Combined sources9
Beta strandi1734 – 1738Combined sources5
Helixi1741 – 1744Combined sources4
Beta strandi1750 – 1756Combined sources7
Turni1757 – 1761Combined sources5
Turni1763 – 1766Combined sources4
Helixi1770 – 1772Combined sources3
Turni1777 – 1781Combined sources5
Beta strandi1786 – 1788Combined sources3
Beta strandi1792 – 1794Combined sources3
Helixi1802 – 1807Combined sources6
Helixi1820 – 1834Combined sources15
Turni1835 – 1837Combined sources3
Helixi1845 – 1850Combined sources6
Beta strandi1860 – 1862Combined sources3
Turni1866 – 1872Combined sources7
Helixi1875 – 1878Combined sources4
Turni1881 – 1884Combined sources4
Helixi1887 – 1895Combined sources9
Beta strandi1902 – 1906Combined sources5
Beta strandi1910 – 1912Combined sources3
Helixi1913 – 1917Combined sources5
Beta strandi1923 – 1926Combined sources4
Helixi1929 – 1948Combined sources20
Turni1952 – 1955Combined sources4
Helixi1962 – 1965Combined sources4
Turni1966 – 1968Combined sources3
Helixi1969 – 1972Combined sources4
Beta strandi1975 – 1978Combined sources4
Beta strandi1981 – 1984Combined sources4
Helixi1985 – 1988Combined sources4
Helixi1991 – 2003Combined sources13
Turni2004 – 2006Combined sources3
Helixi2007 – 2010Combined sources4
Helixi2011 – 2017Combined sources7
Beta strandi2018 – 2023Combined sources6
Beta strandi2026 – 2032Combined sources7
Beta strandi2036 – 2038Combined sources3
Helixi2041 – 2060Combined sources20
Beta strandi2061 – 2063Combined sources3
Helixi2066 – 2068Combined sources3
Beta strandi2070 – 2074Combined sources5
Beta strandi2077 – 2084Combined sources8
Helixi2088 – 2097Combined sources10
Beta strandi2102 – 2104Combined sources3
Turni2105 – 2107Combined sources3
Turni2116 – 2118Combined sources3
Beta strandi2124 – 2128Combined sources5
Beta strandi2130 – 2132Combined sources3
Beta strandi2135 – 2139Combined sources5
Helixi2142 – 2149Combined sources8
Beta strandi2151 – 2153Combined sources3
Helixi2155 – 2157Combined sources3
Helixi2158 – 2169Combined sources12
Helixi2170 – 2172Combined sources3
Helixi2174 – 2184Combined sources11
Helixi2188 – 2191Combined sources4
Helixi2198 – 2208Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AL2X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR6X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR7X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR8X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR9X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1ASJX-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1DGIelectron microscopy22.001599-881[»]
274-341[»]
3342-576[»]
42-69[»]
1FPTX-ray3.00P665-682[»]
1HXSX-ray2.201580-881[»]
270-341[»]
3342-578[»]
42-69[»]
1L1NX-ray2.10A/B1566-1748[»]
1NG7NMR-A/B1457-1515[»]
1NN8electron microscopy15.001580-881[»]
270-341[»]
3342-576[»]
42-69[»]
1PO1X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1PO2X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1POVX-ray2.8002-341[»]
1580-881[»]
3342-579[»]
1RA6X-ray2.00A1749-2209[»]
1RA7X-ray2.35A1749-2209[»]
1RAJX-ray2.50A1817-2209[»]
1RDRX-ray2.40A1749-2209[»]
1TQLX-ray2.30A1749-2209[»]
1VBDX-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1XYRelectron microscopy11.001650-881[»]
297-333[»]
3391-572[»]
5342-353[»]
6355-390[»]
782-95[»]
8621-631[»]
2BBLNMR-A1544-1565[»]
2BBPNMR-A1544-1565[»]
2IJDX-ray3.401/21566-2208[»]
2IJFX-ray3.00A1749-2208[»]
2ILYX-ray2.60A1749-2208[»]
2ILZX-ray2.50A1749-2208[»]
2IM0X-ray2.25A1749-2208[»]
2IM1X-ray2.50A1749-2208[»]
2IM2X-ray2.35A1749-2208[»]
2IM3X-ray2.60A1749-2208[»]
2PLVX-ray2.881580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3EPCelectron microscopy8.001599-881[»]
274-341[»]
3342-576[»]
42-69[»]
3IYBelectron microscopy10.001647-881[»]
3342-572[»]
497-341[»]
3IYCelectron microscopy-1647-881[»]
497-341[»]
3J3Oelectron microscopy11.101580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3J3Pelectron microscopy9.101580-881[»]
270-341[»]
3342-579[»]
3J48electron microscopy5.501580-881[»]
270-341[»]
3342-579[»]
3J8Felectron microscopy3.701580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3J9Felectron microscopy9.001580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3JBCelectron microscopy5.601580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBDelectron microscopy4.701580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBEelectron microscopy4.201580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBFelectron microscopy4.601580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBGelectron microscopy3.801580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3OL7X-ray2.70A/E/I/M1749-2209[»]
4DCDX-ray1.69A1566-1748[»]
4K4SX-ray2.40A/E1749-2209[»]
4K4TX-ray2.75A/E1749-2209[»]
4K4UX-ray2.85A/E1749-2209[»]
4K4VX-ray2.63A/E1749-2209[»]
4K4WX-ray2.69A/E1749-2209[»]
4NLOX-ray2.20A1749-2209[»]
4NLPX-ray2.20A1749-2209[»]
4NLQX-ray2.30A1749-2209[»]
4NLRX-ray2.00A1749-2209[»]
4NLSX-ray2.00A1749-2209[»]
4NLTX-ray2.50A1749-2209[»]
4NLUX-ray2.10A1749-2209[»]
4NLVX-ray2.30A1749-2209[»]
4NLWX-ray2.10A1749-2209[»]
4NLXX-ray2.60A1749-2209[»]
4NLYX-ray2.30A1749-2209[»]
4R0EX-ray3.00A1749-2209[»]
ProteinModelPortaliP03300.
SMRiP03300.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03300.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini882 – 1031Peptidase C3 1Add BLAST150
Domaini1232 – 1388SF3 helicasePROSITE-ProRule annotationAdd BLAST157
Domaini1566 – 1731Peptidase C3 2Add BLAST166
Domaini1975 – 2090RdRp catalyticPROSITE-ProRule annotationAdd BLAST116

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni580 – 600Amphipatic alpha-helixSequence analysisAdd BLAST21
Regioni1457 – 1479DisorderedAdd BLAST23

Sequence similaritiesi

Belongs to the picornaviruses polyprotein family.Curated
Contains 2 peptidase C3 domains.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Family and domain databases

CDDicd00205. rhv_like. 3 hits.
Gene3Di2.60.120.20. 3 hits.
3.40.50.300. 1 hit.
4.10.80.10. 2 hits.
InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR014838. P3A.
IPR000081. Peptidase_C3.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR009003. Peptidase_S1_PA.
IPR003138. Pico_P1A.
IPR002527. Pico_P2B.
IPR001676. Picornavirus_capsid.
IPR033703. Rhv-like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF08727. P3A. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF02226. Pico_P1A. 1 hit.
PF00947. Pico_P2A. 1 hit.
PF01552. Pico_P2B. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 3 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
ProDomiPD001306. Peptidase_C3. 1 hit.
PD649346. Pico_P2B. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF50494. SSF50494. 2 hits.
SSF52540. SSF52540. 1 hit.
SSF89043. SSF89043. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P03300-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYRDSASNA ASKQDFSQDP
60 70 80 90 100
SKFTEPIKDV LIKTAPMLNS PNIEACGYSD RVLQLTLGNS TITTQEAANS
110 120 130 140 150
VVAYGRWPEY LRDSEANPVD QPTEPDVAAC RFYTLDTVSW TKESRGWWWK
160 170 180 190 200
LPDALRDMGL FGQNMYYHYL GRSGYTVHVQ CNASKFHQGA LGVFAVPEMC
210 220 230 240 250
LAGDSNTTTM HTSYQNANPG EKGGTFTGTF TPDNNQTSPA RRFCPVDYLL
260 270 280 290 300
GNGTLLGNAF VFPHQIINLR TNNCATLVLP YVNSLSIDSM VKHNNWGIAI
310 320 330 340 350
LPLAPLNFAS ESSPEIPITL TIAPMCCEFN GLRNITLPRL QGLPVMNTPG
360 370 380 390 400
SNQYLTADNF QSPCALPEFD VTPPIDIPGE VKNMMELAEI DTMIPFDLSA
410 420 430 440 450
TKKNTMEMYR VRLSDKPHTD DPILCLSLSP ASDPRLSHTM LGEILNYYTH
460 470 480 490 500
WAGSLKFTFL FCGFMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG
510 520 530 540 550
LQSSCTMVVP WISNTTYRQT IDDSFTEGGY ISVFYQTRIV VPLSTPREMD
560 570 580 590 600
ILGFVSACND FSVRLLRDTT HIEQKALAQG LGQMLESMID NTVRETVGAA
610 620 630 640 650
TSRDALPNTE ASGPTHSKEI PALTAVETGA TNPLVPSDTV QTRHVVQHRS
660 670 680 690 700
RSESSIESFF ARGACVTIMT VDNPASTTNK DKLFAVWKIT YKDTVQLRRK
710 720 730 740 750
LEFFTYSRFD MELTFVVTAN FTETNNGHAL NQVYQIMYVP PGAPVPEKWD
760 770 780 790 800
DYTWQTSSNP SIFYTYGTAP ARISVPYVGI SNAYSHFYDG FSKVPLKDQS
810 820 830 840 850
AALGDSLYGA ASLNDFGILA VRVVNDHNPT KVTSKIRVYL KPKHIRVWCP
860 870 880 890 900
RPPRAVAYYG PGVDYKDGTL TPLSTKDLTT YGFGHQNKAV YTAGYKICNY
910 920 930 940 950
HLATQDDLQN AVNVMWSRDL LVTESRAQGT DSIARCNCNA GVYYCESRRK
960 970 980 990 1000
YYPVSFVGPT FQYMEANNYY PARYQSHMLI GHGFASPGDC GGILRCHHGV
1010 1020 1030 1040 1050
IGIITAGGEG LVAFSDIRDL YAYEEEAMEQ GITNYIESLG AAFGSGFTQQ
1060 1070 1080 1090 1100
ISDKITELTN MVTSTITEKL LKNLIKIISS LVIITRNYED TTTVLATLAL
1110 1120 1130 1140 1150
LGCDASPWQW LRKKACDVLE IPYVIKQGDS WLKKFTEACN AAKGLEWVSN
1160 1170 1180 1190 1200
KISKFIDWLK EKIIPQARDK LEFVTKLRQL EMLENQISTI HQSCPSQEHQ
1210 1220 1230 1240 1250
EILFNNVRWL SIQSKRFAPL YAVEAKRIQK LEHTINNYIQ FKSKHRIEPV
1260 1270 1280 1290 1300
CLLVHGSPGT GKSVATNLIA RAIAERENTS TYSLPPDPSH FDGYKQQGVV
1310 1320 1330 1340 1350
IMDDLNQNPD GADMKLFCQM VSTVEFIPPM ASLEEKGILF TSNYVLASTN
1360 1370 1380 1390 1400
SSRISPPTVA HSDALARRFA FDMDIQVMNE YSRDGKLNMA MATEMCKNCH
1410 1420 1430 1440 1450
QPANFKRCCP LVCGKAIQLM DKSSRVRYSI DQITTMIINE RNRRSNIGNC
1460 1470 1480 1490 1500
MEALFQGPLQ YKDLKIDIKT SPPPECINDL LQAVDSQEVR DYCEKKGWIV
1510 1520 1530 1540 1550
NITSQVQTER NINRAMTILQ AVTTFAAVAG VVYVMYKLFA GHQGAYTGLP
1560 1570 1580 1590 1600
NKKPNVPTIR TAKVQGPGFD YAVAMAKRNI VTATTSKGEF TMLGVHDNVA
1610 1620 1630 1640 1650
ILPTHASPGE SIVIDGKEVE ILDAKALEDQ AGTNLEITII TLKRNEKFRD
1660 1670 1680 1690 1700
IRPHIPTQIT ETNDGVLIVN TSKYPNMYVP VGAVTEQGYL NLGGRQTART
1710 1720 1730 1740 1750
LMYNFPTRAG QCGGVITCTG KVIGMHVGGN GSHGFAAALK RSYFTQSQGE
1760 1770 1780 1790 1800
IQWMRPSKEV GYPIINAPSK TKLEPSAFHY VFEGVKEPAV LTKNDPRLKT
1810 1820 1830 1840 1850
DFEEAIFSKY VGNKITEVDE YMKEAVDHYA GQLMSLDINT EQMCLEDAMY
1860 1870 1880 1890 1900
GTDGLEALDL STSAGYPYVA MGKKKRDILN KQTRDTKEMQ KLLDTYGINL
1910 1920 1930 1940 1950
PLVTYVKDEL RSKTKVEQGK SRLIEASSLN DSVAMRMAFG NLYAAFHKNP
1960 1970 1980 1990 2000
GVITGSAVGC DPDLFWSKIP VLMEEKLFAF DYTGYDASLS PAWFEALKMV
2010 2020 2030 2040 2050
LEKIGFGDRV DYIDYLNHSH HLYKNKTYCV KGGMPSGCSG TSIFNSMINN
2060 2070 2080 2090 2100
LIIRTLLLKT YKGIDLDHLK MIAYGDDVIA SYPHEVDASL LAQSGKDYGL
2110 2120 2130 2140 2150
TMTPADKSAT FETVTWENVT FLKRFFRADE KYPFLIHPVM PMKEIHESIR
2160 2170 2180 2190 2200
WTKDPRNTQD HVRSLCLLAW HNGEEEYNKF LAKIRSVPIG RALLLPEYST

LYRRWLDSF
Length:2,209
Mass (Da):246,540
Last modified:January 23, 2007 - v3
Checksum:iDF1754F87F2E97D6
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti242 – 264RFCPV…FVFPH → SSARWITSLEMARCWGMPLC SA in CAA24446 (PubMed:6272282).CuratedAdd BLAST23
Sequence conflicti287I → L in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti309A → V in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti420 – 422DDP → AAS in CAA24446 (PubMed:6272282).Curated3
Sequence conflicti464F → S in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti515T → S in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti855 – 856AV → QL in CAA24446 (PubMed:6272282).Curated2
Sequence conflicti972A → V in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti985A → E in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti1140 – 1141NA → QR in CAA24446 (PubMed:6272282).Curated2
Sequence conflicti1619V → A in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti1626 – 1627AL → VF in CAA24446 (PubMed:6272282).Curated2
Sequence conflicti1635L → F in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti1682G → R in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti1722 – 1730VIGMHVGGN → SSGCMLVD in CAA24446 (PubMed:6272282).Curated9
Sequence conflicti1743Y → L in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti1752Q → P in CAA24446 (PubMed:6272282).Curated1
Sequence conflicti1759 – 1760EV → DA in CAA24446 (PubMed:6272282).Curated2
Sequence conflicti1840T → I in CAA24446 (PubMed:6272282).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01149 Genomic RNA. Translation: CAA24461.1.
V01148 Genomic RNA. Translation: CAA24446.1.
PIRiA03898. GNNY2P.
A93258. GNNY1P.
RefSeqiNP_041277.1. NC_002058.3.

Genome annotation databases

GeneIDi919920.
KEGGivg:919920.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure associated with cellular receptor

Virus Particle ExploreR db

Icosahedral capsid structure associated with cellular receptor

Virus Particle ExploreR db

Icosahedral capsid structure in complex with R80633, an inhibitor of viral replication

Virus Particle ExploreR db

Icosahedral capsid structure in complex with R77975, an inhibitor of viral replication

Virus Particle ExploreR db

Icosahedral empty capsid structure

Virus Particle ExploreR db

Icosahedral capsid structure complexed with R78206

Virus Particle ExploreR db

Icosahedral capsid structure

Virus Particle ExploreR db

Icosahedral capsid structure of 135S cell entry intermediate

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01149 Genomic RNA. Translation: CAA24461.1.
V01148 Genomic RNA. Translation: CAA24446.1.
PIRiA03898. GNNY2P.
A93258. GNNY1P.
RefSeqiNP_041277.1. NC_002058.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AL2X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR6X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR7X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR8X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1AR9X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1ASJX-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1DGIelectron microscopy22.001599-881[»]
274-341[»]
3342-576[»]
42-69[»]
1FPTX-ray3.00P665-682[»]
1HXSX-ray2.201580-881[»]
270-341[»]
3342-578[»]
42-69[»]
1L1NX-ray2.10A/B1566-1748[»]
1NG7NMR-A/B1457-1515[»]
1NN8electron microscopy15.001580-881[»]
270-341[»]
3342-576[»]
42-69[»]
1PO1X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1PO2X-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1POVX-ray2.8002-341[»]
1580-881[»]
3342-579[»]
1RA6X-ray2.00A1749-2209[»]
1RA7X-ray2.35A1749-2209[»]
1RAJX-ray2.50A1817-2209[»]
1RDRX-ray2.40A1749-2209[»]
1TQLX-ray2.30A1749-2209[»]
1VBDX-ray2.901580-881[»]
270-341[»]
3342-579[»]
42-69[»]
1XYRelectron microscopy11.001650-881[»]
297-333[»]
3391-572[»]
5342-353[»]
6355-390[»]
782-95[»]
8621-631[»]
2BBLNMR-A1544-1565[»]
2BBPNMR-A1544-1565[»]
2IJDX-ray3.401/21566-2208[»]
2IJFX-ray3.00A1749-2208[»]
2ILYX-ray2.60A1749-2208[»]
2ILZX-ray2.50A1749-2208[»]
2IM0X-ray2.25A1749-2208[»]
2IM1X-ray2.50A1749-2208[»]
2IM2X-ray2.35A1749-2208[»]
2IM3X-ray2.60A1749-2208[»]
2PLVX-ray2.881580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3EPCelectron microscopy8.001599-881[»]
274-341[»]
3342-576[»]
42-69[»]
3IYBelectron microscopy10.001647-881[»]
3342-572[»]
497-341[»]
3IYCelectron microscopy-1647-881[»]
497-341[»]
3J3Oelectron microscopy11.101580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3J3Pelectron microscopy9.101580-881[»]
270-341[»]
3342-579[»]
3J48electron microscopy5.501580-881[»]
270-341[»]
3342-579[»]
3J8Felectron microscopy3.701580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3J9Felectron microscopy9.001580-881[»]
270-341[»]
3342-579[»]
42-69[»]
3JBCelectron microscopy5.601580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBDelectron microscopy4.701580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBEelectron microscopy4.201580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBFelectron microscopy4.601580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3JBGelectron microscopy3.801580-881[»]
270-341[»]
3342-578[»]
42-69[»]
3OL7X-ray2.70A/E/I/M1749-2209[»]
4DCDX-ray1.69A1566-1748[»]
4K4SX-ray2.40A/E1749-2209[»]
4K4TX-ray2.75A/E1749-2209[»]
4K4UX-ray2.85A/E1749-2209[»]
4K4VX-ray2.63A/E1749-2209[»]
4K4WX-ray2.69A/E1749-2209[»]
4NLOX-ray2.20A1749-2209[»]
4NLPX-ray2.20A1749-2209[»]
4NLQX-ray2.30A1749-2209[»]
4NLRX-ray2.00A1749-2209[»]
4NLSX-ray2.00A1749-2209[»]
4NLTX-ray2.50A1749-2209[»]
4NLUX-ray2.10A1749-2209[»]
4NLVX-ray2.30A1749-2209[»]
4NLWX-ray2.10A1749-2209[»]
4NLXX-ray2.60A1749-2209[»]
4NLYX-ray2.30A1749-2209[»]
4R0EX-ray3.00A1749-2209[»]
ProteinModelPortaliP03300.
SMRiP03300.
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

BindingDBiP03300.
ChEMBLiCHEMBL5127.

Protein family/group databases

MEROPSiN08.001.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi919920.
KEGGivg:919920.

Miscellaneous databases

EvolutionaryTraceiP03300.
PMAP-CutDBP03299.

Family and domain databases

CDDicd00205. rhv_like. 3 hits.
Gene3Di2.60.120.20. 3 hits.
3.40.50.300. 1 hit.
4.10.80.10. 2 hits.
InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR014838. P3A.
IPR000081. Peptidase_C3.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR009003. Peptidase_S1_PA.
IPR003138. Pico_P1A.
IPR002527. Pico_P2B.
IPR001676. Picornavirus_capsid.
IPR033703. Rhv-like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF08727. P3A. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF02226. Pico_P1A. 1 hit.
PF00947. Pico_P2A. 1 hit.
PF01552. Pico_P2B. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 3 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
ProDomiPD001306. Peptidase_C3. 1 hit.
PD649346. Pico_P2B. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF50494. SSF50494. 2 hits.
SSF52540. SSF52540. 1 hit.
SSF89043. SSF89043. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_POL1M
AccessioniPrimary (citable) accession number: P03300
Secondary accession number(s): P03299
, Q84879, Q84880, Q89679
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 187 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Caution

Protein 3A: Has been proposed to interact with host LIS1/NUF (PubMed:16138011), but this has not been confirmed by other studies (PubMed:21345960).2 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.