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Protein

Replicase polyprotein 1ab

Gene

rep

Organism
Avian infectious bronchitis virus (strain M41) (IBV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products.
The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (By similarity).By similarity
The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).PROSITE-ProRule annotation
The peptide p16 might be involved in the EGF signaling pathway.By similarity
The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G) (By similarity).By similarity
The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.By similarity
Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.By similarity
Nsp9 is a ssRNA-binding protein.By similarity
NendoU is a Mn2+-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.By similarity

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
ATP + H2O = ADP + phosphate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei1276 – 12761For PL-PRO activityPROSITE-ProRule annotation
Active sitei1439 – 14391For PL-PRO activityPROSITE-ProRule annotation
Active sitei2822 – 28221For 3CL-PRO activityPROSITE-ProRule annotation
Active sitei2924 – 29241For 3CL-PRO activityPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1355 – 139238C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri3860 – 388021By similarityAdd
BLAST
Zinc fingeri3906 – 391914By similarityAdd
BLAST
Nucleotide bindingi5152 – 51598ATPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Helicase, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Activation of host autophagy by virus, Host-virus interaction, Viral RNA replication

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Protein family/group databases

MEROPSiC30.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Replicase polyprotein 1ab
Short name:
pp1ab
Alternative name(s):
ORF1ab polyprotein
Cleaved into the following 14 chains:
Non-structural protein 2
Short name:
nsp2
Alternative name(s):
p87
Non-structural protein 3 (EC:3.4.22.-)
Short name:
nsp3
Alternative name(s):
Papain-like proteinase
Short name:
PL-PRO
p195
Non-structural protein 4
Short name:
nsp4
Alternative name(s):
Peptide HD2
p41
3C-like proteinase (EC:3.4.22.-)
Short name:
3CL-PRO
Short name:
3CLp
Alternative name(s):
M-PRO
nsp5
p33
Non-structural protein 6
Short name:
nsp6
Alternative name(s):
p34
Non-structural protein 7
Short name:
nsp7
Alternative name(s):
p9
Non-structural protein 8
Short name:
nsp8
Alternative name(s):
p24
Non-structural protein 9
Short name:
nsp9
Alternative name(s):
p10
Non-structural protein 10
Short name:
nsp10
Alternative name(s):
Growth factor-like peptide
Short name:
GFL
p16
RNA-directed RNA polymerase (EC:2.7.7.48)
Short name:
Pol
Short name:
RdRp
Alternative name(s):
nsp12
p100
Helicase (EC:3.6.4.12, EC:3.6.4.13)
Short name:
Hel
Alternative name(s):
nsp13
p68
Exoribonuclease (EC:3.1.13.-)
Short name:
ExoN
Alternative name(s):
nsp14
p58
Alternative name(s):
NendoU
nsp15
p39
Alternative name(s):
nsp16
p35
Gene namesi
Name:rep
ORF Names:1a-1b
OrganismiAvian infectious bronchitis virus (strain M41) (IBV)
Taxonomic identifieri11127 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageNidoviralesCoronaviridaeCoronavirinaeGammacoronavirus
Virus hostiGallus gallus (Chicken) [TaxID: 9031]
Proteomesi
  • UP000007642 Componenti: Genome

Subcellular locationi

Non-structural protein 7 :
  • Host cytoplasmhost perinuclear region By similarity

  • Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Non-structural protein 8 :
  • Host cytoplasmhost perinuclear region By similarity

  • Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Non-structural protein 9 :
  • Host cytoplasmhost perinuclear region By similarity

  • Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Non-structural protein 10 :
  • Host cytoplasmhost perinuclear region By similarity

  • Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Helicase :

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei1723 – 174321HelicalSequence analysisAdd
BLAST
Transmembranei1753 – 177321HelicalSequence analysisAdd
BLAST
Transmembranei1846 – 186621HelicalSequence analysisAdd
BLAST
Transmembranei1889 – 190921HelicalSequence analysisAdd
BLAST
Transmembranei2283 – 230321HelicalSequence analysisAdd
BLAST
Transmembranei2373 – 239321HelicalSequence analysisAdd
BLAST
Transmembranei2562 – 258221HelicalSequence analysisAdd
BLAST
Transmembranei2591 – 261121HelicalSequence analysisAdd
BLAST
Transmembranei2614 – 263421HelicalSequence analysisAdd
BLAST
Transmembranei2646 – 266621HelicalSequence analysisAdd
BLAST
Transmembranei3103 – 312321HelicalSequence analysisAdd
BLAST
Transmembranei3124 – 314421HelicalSequence analysisAdd
BLAST
Transmembranei3154 – 317421HelicalSequence analysisAdd
BLAST
Transmembranei3191 – 321121HelicalSequence analysisAdd
BLAST
Transmembranei3222 – 324221HelicalSequence analysisAdd
BLAST
Transmembranei3260 – 328021HelicalSequence analysisAdd
BLAST
Transmembranei3299 – 331921HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host cytoplasm, Host membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 673673Non-structural protein 2By similarityPRO_0000283889Add
BLAST
Chaini674 – 22671594Non-structural protein 3By similarityPRO_0000283890Add
BLAST
Chaini2268 – 2781514Non-structural protein 4By similarityPRO_0000283891Add
BLAST
Chaini2782 – 30883073C-like proteinaseBy similarityPRO_0000283892Add
BLAST
Chaini3089 – 3381293Non-structural protein 6By similarityPRO_0000283893Add
BLAST
Chaini3382 – 346483Non-structural protein 7By similarityPRO_0000283894Add
BLAST
Chaini3465 – 3674210Non-structural protein 8By similarityPRO_0000283895Add
BLAST
Chaini3675 – 3785111Non-structural protein 9By similarityPRO_0000283896Add
BLAST
Chaini3786 – 3930145Non-structural protein 10By similarityPRO_0000283897Add
BLAST
Chaini3931 – 4870940RNA-directed RNA polymeraseBy similarityPRO_0000283898Add
BLAST
Chaini4871 – 5470600HelicaseBy similarityPRO_0000283899Add
BLAST
Chaini5471 – 5991521ExoribonucleaseBy similarityPRO_0000283900Add
BLAST
Chaini5992 – 6329338Uridylate-specific endoribonucleaseBy similarityPRO_0000283901Add
BLAST
Chaini6330 – 6631302Putative 2'-O-methyl transferaseBy similarityPRO_0000283902Add
BLAST

Post-translational modificationi

Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei673 – 6742Cleavage; by PL-PROBy similarity
Sitei2267 – 22682Cleavage; by PL-PROBy similarity
Sitei2781 – 27822Cleavage; by 3CL-PROBy similarity
Sitei3088 – 30892Cleavage; by 3CL-PROBy similarity
Sitei3381 – 33822Cleavage; by 3CL-PROBy similarity
Sitei3464 – 34652Cleavage; by 3CL-PROBy similarity
Sitei3674 – 36752Cleavage; by 3CL-PROBy similarity
Sitei3785 – 37862Cleavage; by 3CL-PROBy similarity
Sitei3930 – 39312Cleavage; by 3CL-PROBy similarity
Sitei4870 – 48712Cleavage; by 3CL-PROBy similarity
Sitei5470 – 54712Cleavage; by 3CL-PROBy similarity
Sitei5991 – 59922Cleavage; by 3CL-PROBy similarity
Sitei6329 – 63302Cleavage; by 3CL-PROBy similarity

Interactioni

Subunit structurei

3CL-PRO exists as monomer and homodimer. The three peptides nsp2, nsp3 and nsp4 may form a complex. Nsp9 is a dimer. Eight copies of nsp7 and eight copies of nsp8 assemble to form a heterohexadecamer. Nsp10 forms a dodecamer (By similarity).By similarity

Structurei

Secondary structure

1
6631
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2792 – 27954Combined sources
Beta strandi2798 – 28025Combined sources
Beta strandi2807 – 28137Combined sources
Beta strandi2816 – 28205Combined sources
Helixi2821 – 28244Combined sources
Turni2829 – 28313Combined sources
Helixi2832 – 28387Combined sources
Helixi2841 – 28433Combined sources
Beta strandi2845 – 28473Combined sources
Beta strandi2856 – 28627Combined sources
Beta strandi2865 – 28728Combined sources
Beta strandi2879 – 28824Combined sources
Beta strandi2890 – 28978Combined sources
Beta strandi2900 – 29089Combined sources
Beta strandi2927 – 29326Combined sources
Beta strandi2935 – 294511Combined sources
Beta strandi2950 – 29545Combined sources
Helixi2961 – 29633Combined sources
Beta strandi2966 – 29694Combined sources
Helixi2980 – 299314Combined sources
Helixi3012 – 30198Combined sources
Turni3020 – 30234Combined sources
Helixi3031 – 30399Combined sources
Helixi3044 – 305613Combined sources
Beta strandi3066 – 30683Combined sources
Helixi3075 – 30806Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q6DX-ray2.35A/B/C2783-3088[»]
2Q6FX-ray2.00A/B2783-3088[»]
ProteinModelPortaliP0C6Y3.
SMRiP0C6Y3. Positions 2787-3088, 3799-3920.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C6Y3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1005 – 1181177MacroPROSITE-ProRule annotationAdd
BLAST
Domaini1238 – 1499262Peptidase C16PROSITE-ProRule annotationAdd
BLAST
Domaini2782 – 3088307Peptidase C30PROSITE-ProRule annotationAdd
BLAST
Domaini4550 – 4712163RdRp catalyticPROSITE-ProRule annotationAdd
BLAST
Domaini4871 – 495484CV MBDAdd
BLAST
Domaini5127 – 5307181(+)RNA virus helicase ATP-bindingAdd
BLAST
Domaini5308 – 5479172(+)RNA virus helicase C-terminalAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1723 – 1909187HD1By similarityAdd
BLAST
Regioni2283 – 2666384HD2By similarityAdd
BLAST
Regioni2887 – 3319433HD3By similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1729 – 17346Poly-Phe

Domaini

The hydrophobic domains (HD) could mediate the membrane association of the replication complex and thereby alter the architecture of the host cell membrane.

Sequence similaritiesi

Contains 1 Macro domain.PROSITE-ProRule annotation
Contains 1 peptidase C16 domain.PROSITE-ProRule annotation
Contains 1 peptidase C30 domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1355 – 139238C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri3860 – 388021By similarityAdd
BLAST
Zinc fingeri3906 – 391914By similarityAdd
BLAST

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix, Zinc-finger

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR032505. Corona_NSP4_C.
IPR009461. Coronavirus_NSP16.
IPR027352. CV_MBD_dom.
IPR002589. Macro_dom.
IPR009466. NSP11.
IPR014828. NSP7.
IPR014829. NSP8.
IPR014822. NSP9.
IPR027417. P-loop_NTPase.
IPR008740. Peptidase_C30.
IPR013016. Peptidase_C30/C16.
IPR009003. Peptidase_S1_PA.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009469. RNA_pol_N_coronovir.
IPR018995. RNA_synth_NSP10_coronavirus.
IPR029063. SAM-dependent_MTases.
IPR014827. Viral_protease.
[Graphical view]
PfamiPF16348. Corona_NSP4_C. 1 hit.
PF06478. Corona_RPol_N. 1 hit.
PF01661. Macro. 1 hit.
PF09401. NSP10. 1 hit.
PF06471. NSP11. 1 hit.
PF06460. NSP13. 1 hit.
PF08716. nsp7. 1 hit.
PF08717. nsp8. 1 hit.
PF08710. nsp9. 1 hit.
PF05409. Peptidase_C30. 1 hit.
PF00680. RdRP_1. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF08715. Viral_protease. 1 hit.
[Graphical view]
SMARTiSM00506. A1pp. 1 hit.
[Graphical view]
SUPFAMiSSF101816. SSF101816. 1 hit.
SSF144246. SSF144246. 1 hit.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51653. CV_MBD. 1 hit.
PS51442. M_PRO. 1 hit.
PS51154. MACRO. 1 hit.
PS51124. PEPTIDASE_C16. 1 hit.
PS51657. PSRV_HELICASE. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform Replicase polyprotein 1ab (identifier: P0C6Y3-1) [UniParc]FASTAAdd to basket

Also known as: pp1ab

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MASSLKQGVS PKLRDVILVS KDIPEQLCDA LFFYTSHNPK DYADAFAVRQ
60 70 80 90 100
KFDRNLQTGK QFKFETVCGL FLLKGVDKIT PGVPAKVLKA TSKLADLEDI
110 120 130 140 150
FGVSPFARKY RELLKTACQW SLTVETLDAR AQTLDEIFDP TEILWLQVAA
160 170 180 190 200
KIQVSAMAMR RLVGEVTAKV MDALGSNMSA LFQIFKQQIV RIFQKALAIF
210 220 230 240 250
ENVSELPQRI AALKMAFAKC AKSITVVVME RTLVVREFAG TCLASINGAV
260 270 280 290 300
AKFFEELPNG FMGAKIFTTL AFFREAAVKI VDNIPNAPRG TKGFEVVGNA
310 320 330 340 350
KGTQVVVRGM RNDLTLLDQK AEIPVESEGW SAILGGHLCY VFKSGDRFYA
360 370 380 390 400
APLSGNFALH DVHCCERVVC LSDGVTPEIN DGLILAAIYS SFSVAELVAA
410 420 430 440 450
IKRGEPFKFL GHKFVYAKDA AVSFTLAKAA TIADVLKLFQ SARVKVEDVW
460 470 480 490 500
SSLTEKSFEF WRLAYGKVRN LEEFVKTCFC KAQMAIVILA TVLGEGIWHL
510 520 530 540 550
VSQVIYKVGG LFTKVVDFCE KYWKGFCAQL KRAKLIVTET LCVLKGVAQH
560 570 580 590 600
CFQLLLDAIQ FMYKSFKKCA LGRIHGDLLF WKGGVHKIIQ EGDEIWFDAI
610 620 630 640 650
DSIDVEDLGV VQEKLIDFDV CDNVTLPENQ PGHMVQIEDD GKNYMFFRFK
660 670 680 690 700
KDENIYYTPM SQLGAINVVC KAGGKTVTFG ETTVQEIPPP DVVFIKVSIE
710 720 730 740 750
CCGEPWNTIF KKAYKEPIEV ETDLTVEQLL SVVYEKMCDD LKLFPEAPEP
760 770 780 790 800
PPFENVTLVD KNGKDLDCIK SCHLIYRDYE SDDDIEEEDA EECDTDSGDA
810 820 830 840 850
EECDTNLECE EEDEDTKVLA LIQDPASNKY PLPLDDDYSV YNGCIVHKDA
860 870 880 890 900
LDVVNLPSGE ETFVVNNCFE GAVKALPQKV IDVLGDWGEA VDAQEQLCQQ
910 920 930 940 950
ESTRVISEKS VEGFTGSCDA MAEQAIVEEQ EIVPVVEQSQ DVVVFTPADL
960 970 980 990 1000
EVVKETAEEV DEFILISAVP KEEVVSQEKE EPQVEQEPTL VVKAQREKKA
1010 1020 1030 1040 1050
KKFKVKPATC EKPKFLEYKT CVGDLAVVIA KALDEFKEFC IVNAANEHMS
1060 1070 1080 1090 1100
HGGGVAKAIA DFCGPDFVEY CADYVKKHGP QQKLVTPSFV KGIQCVNNVV
1110 1120 1130 1140 1150
GPRHGDSNLR EKLVAAYKSV LVGGVVNYVV PVLSSGIFGV DFKISIDAMR
1160 1170 1180 1190 1200
EAFKGCAIRV LLFSLSQEHI DYFDATCKQK TIYLTEDGVK YRSVVLKPGD
1210 1220 1230 1240 1250
SLGQFGQVFA RNKVVFSADD VEDKEILFIP TTDKTILEYY GLDAQKYVTY
1260 1270 1280 1290 1300
LQTLAQKWDV QYRDNFVILE WRDGNCWISS AIVLLQAAKI RFKGFLAEAW
1310 1320 1330 1340 1350
AKLLGGDPTD FVAWCYASCN AKVGDFSDAN WLLANLAEHF DADYTNALLK
1360 1370 1380 1390 1400
KCVSCNCGVK SYELRGLEAC IQPVRAPNLL HFKTQYSNCP TCGASSTDEV
1410 1420 1430 1440 1450
IEASLPYLLL FATDGPATVD CDENAVGTVV FIGSTNSGHC YTQADGKAFD
1460 1470 1480 1490 1500
NLAKDRKFGR KSPYITAMYT RFSLRSENPL LVVEHSKGKA KVVKEDVSNL
1510 1520 1530 1540 1550
ATSSKASFDD LTDFEQWYDS NIYESLKVQE TPDNLDEYVS FTTKEDSKLP
1560 1570 1580 1590 1600
LTLKVRGIKS VVDFRSKDGF TYKLTPDTDE NSKTPVYYPV LDSISLRAIW
1610 1620 1630 1640 1650
VEGSANFVVG HPNYYSKSLR IPTFWENAES FVKMGYKIDG VTMGLWRAEH
1660 1670 1680 1690 1700
LNKPNLERIF NIAKKAIVGS SVVTTQCGKI LVKAATYVAD KVGDGVVRNI
1710 1720 1730 1740 1750
TDRIKGLCGF TRGHFEKKMS LQFLKTLVFF FFYFLKASSK SLVSSYKIVL
1760 1770 1780 1790 1800
CKVVFATLLI VWFIYTSNPV VFTGIRVLDF LFEGSLCGPY NDYGKDSFDV
1810 1820 1830 1840 1850
LRYCAGDFTC RVCLHDRDSL HLYKHAYSVE QIYKDAASGI NFNWNWLYLV
1860 1870 1880 1890 1900
FLILFVKPVA GFVIICYCVK YLVLSSTVLQ TGVGFLDWFV KTVFTHFNFM
1910 1920 1930 1940 1950
GAGFYFWLFY KIYVQVHHIL YCKDVTCEVC KRVARSNRQE VSVVVGGRKQ
1960 1970 1980 1990 2000
IVHVYTNSGY NFCKRHNWYC RNCDDYGHQN TFMSPEVAGE LSEKLKRHVK
2010 2020 2030 2040 2050
PTAYAYHVVY EACVVDDFVN LKYKAAIPGK DNASSAVKCF SVTDFLKKAV
2060 2070 2080 2090 2100
FLKEALKCEQ ISNDGFIVCN TQSAHALEEA KNAAVYYAQY LCKPILILDQ
2110 2120 2130 2140 2150
ALYEQLIVEP VSKSVIDKVC SILSNIISVD TAALNYKAGT LRDALLSITK
2160 2170 2180 2190 2200
DEEAVDMAIF CHNHEVEYTG DGFTNVIPSY GMDTDKLTPR DRGFLINADA
2210 2220 2230 2240 2250
SIANLRVKNA PPVVWKFSDL IKLSDSCLKY LISATVKSGG RFFITKSGAK
2260 2270 2280 2290 2300
QVISCHTQKL LVEKKAGGVI NNTFKWFMSC FKWLFVFYIL FTACCLGYYY
2310 2320 2330 2340 2350
MEMNKSFVHP MYDVNSTLHV EGFKVIDKGV IREIVSEDNC FSNKFVNFDA
2360 2370 2380 2390 2400
FWGKSYENNK NCPIVTVVID GDGTVAVGVP GFVSWVMDGV MFVHMTQTDR
2410 2420 2430 2440 2450
RPWYIPTWFN REIVGYTQDS IITEGSFYTS IALFSARCLY LTASNTPQLY
2460 2470 2480 2490 2500
CFNGDNDAPG ALPFGSIIPH RVYFQPNGVR LIVPQQILHT PYIVKFVSDS
2510 2520 2530 2540 2550
YCRGSVCEYT KPGYCVSLDS QWVLFNDEYI SKPGVFCGST VRELMFNMVS
2560 2570 2580 2590 2600
TFFTGVNPNI YIQLATMFLI LVVIVLIFAM VIKFQGVFKA YATIVFTIML
2610 2620 2630 2640 2650
VWVINAFVLC VHSYNSVLAV ILLVLYCYAS MVTSRNTAII MHCWLVFTFG
2660 2670 2680 2690 2700
LIVPTWLACC YLGFILYMYT PLVFWCYGTT KNTRKLYDGN EFVGNYDLAA
2710 2720 2730 2740 2750
KSTFVIRGTE FVKLTNEIGD KFEAYLSAYA RLKYYSGTGS EQDYLQACRA
2760 2770 2780 2790 2800
WLAYALDQYR NSGVEVVYTP PRYSIGVSRL QAGFKKLVSP SSAVEKCIVS
2810 2820 2830 2840 2850
VSYRGNNLNG LWLGDSIYCP RHVLGKFSGD QWGDVLNLAN NHEFEVVTQN
2860 2870 2880 2890 2900
GVTLNVVSRR LKGAVLILQT AVANAETPKY KFVKANCGDS FTIACSYGGT
2910 2920 2930 2940 2950
VIGLYPVTMR SNGTIRASFL AGACGSVGFN IEKGVVNFFY MHHLELPNAL
2960 2970 2980 2990 3000
HTGTDLMGEF YGGYVDEEVA QRVPPDNLVT NNIVAWLYAA IISVKESSFS
3010 3020 3030 3040 3050
QPKWLESTTV SIEDYNRWAS DNGFTPFSTS TAITKLSAIT GVDVCKLLRT
3060 3070 3080 3090 3100
IMVKSAQWGS DPILGQYNFE DELTPESVFN QVGGVRLQSS FVRKATSWFW
3110 3120 3130 3140 3150
SRCVLACFLF VLCAIVLFTA VPLKFYVHAA VILLMAVLFI SFTVKHVMAY
3160 3170 3180 3190 3200
MDTFLLPTLI TVIIGVCAEV PFIYNTLISQ VVIFLSQWYD PVVFDTMVPW
3210 3220 3230 3240 3250
MLLPLVLYTA FKCVQGCYMN SFNTSLLMLY QFMKLGFVIY TSSNTLTAYT
3260 3270 3280 3290 3300
EGNWELFFEL VHTIVLANVS SNSLIGLIVF KCAKWMLYYC NATYFNNYVL
3310 3320 3330 3340 3350
MAVMVNGIGW LCTCYFGLYW WVNKVFGLTL GKYNFKVSVD QYRYMCLHKV
3360 3370 3380 3390 3400
NPPKTVWEVF TTNILIQGIG GDRVLPIATV QSKLSDVKCT TVVLMQLLTK
3410 3420 3430 3440 3450
LNVEANSKMH AYLVELHNKI LASDDVGECM DNLLGMLITL FCIDSTIDLG
3460 3470 3480 3490 3500
EYCDDILKRS TVLQSVTQEF SHIPSYAEYE RAKSIYEKVL ADSKNGGVTQ
3510 3520 3530 3540 3550
QELAAYRKAA NIAKSVFDRD LAVQKKLDSM AERAMTTMYK EARVTDRRAK
3560 3570 3580 3590 3600
LVSSLHALLF SMLKKIDSEK LNVLFDQANS GVVPLATVPI VCSNKLTLVI
3610 3620 3630 3640 3650
PDPETWVKCV EGVHVTYSTV VWNIDCVTDA DGTELHPTST GSGLTYCISG
3660 3670 3680 3690 3700
DNIAWPLKVN LTRNGHNKVD VALQNNELMP HGVKTKACVA GVDQAHCSVE
3710 3720 3730 3740 3750
SKCYYTSISG SSVVAAITSS NPNLKVASFL NEAGNQIYVD LDPPCKFGMK
3760 3770 3780 3790 3800
VGDKVEVVYL YFIKNTRSIV RGMVLGAISN VVVLQSKGHE TEEVDAVGIL
3810 3820 3830 3840 3850
SLCSFAVDPA DTYCKYVAAG NQPLGNCVKM LTVHNGSGFA ITSKPSPTPD
3860 3870 3880 3890 3900
QDSYGGASVC LYCRAHIAHP GGAGNLDGRC QFKGSFVQIP TTEKDPVGFC
3910 3920 3930 3940 3950
LRNKVCTVCQ CWIGYGCQCD SLRQPKPSVQ SVAVASGFDK NYLNRVRGSS
3960 3970 3980 3990 4000
EARLIPLANG CDPDVVKRAF DVCNKESAGM FQNLKRNCAR FQEVRDTEDG
4010 4020 4030 4040 4050
NLEYCDSYFV VKQTTPSNYE HEKACYEDLK SEVTADHDFF VFNKNIYNIS
4060 4070 4080 4090 4100
RQRLTKYTMM DFCYALRHFD PKDCEVLKEI LVTYGCIEDY HPKWFEENKD
4110 4120 4130 4140 4150
WYDPIENPKY YAMLAKMGPI VRRALLNAIE FGNLMVEKGY VGVITLDNQD
4160 4170 4180 4190 4200
LNGKFYDFGD FQKTAPGAGV PVFDTYYSYM MPIIAMTDAL APERYFEYDV
4210 4220 4230 4240 4250
HKGYKSYDLL KYDYTEEKQD LFQKYFKYWD QEYHPNCRDC SDDRCLIHCA
4260 4270 4280 4290 4300
NFNILFSTLV PQTSFGNLCR KVFVDGVPFI ATCGYHSKEL GVIMNQDNTM
4310 4320 4330 4340 4350
SFSKMGLSQL MQFVGDPALL VGTSNKLVDL RTSCFSVCAL ASGITHQTVK
4360 4370 4380 4390 4400
PGHFNKDFYD FAEKAGMFKE GSSIPLKHFF YPQTGNAAIN DYDYYRYNRP
4410 4420 4430 4440 4450
TMFDIRQLLF CLEVTSKYFE CYEGGCIPAS QVVVNNLDKS AGYPFNKFGK
4460 4470 4480 4490 4500
ARLYYEMSLE EQDQLFESTK KNVLPTITQM NLKYAISAKN RARTVAGVSI
4510 4520 4530 4540 4550
LSTMTNRQFH QKILKSIVNT RNAPVVIGTT KFYGGWDNML RNLIQGVEDP
4560 4570 4580 4590 4600
ILMGWDYPKC DRAMPNLLRI AASLVLARKH TNCCTWSERV YRLYNECAQV
4610 4620 4630 4640 4650
LSETVLATGG IYVKPGGTSS GDATTAYANS VFNIIQATSA NVARLLSVIT
4660 4670 4680 4690 4700
RDIVYDDIKS LQYELYQQVY RRVNFDPAFV EKFYSYLCKN FSLMILSDDG
4710 4720 4730 4740 4750
VVCYNNTLAK QGLVADISGF REVLYYQNNV FMADSKCWVE PDLEKGPHEF
4760 4770 4780 4790 4800
CSQHTMLVEV DGEPRYLPYP DPSRILCACV FVDDLDKTES VAVMERYIAL
4810 4820 4830 4840 4850
AIDAYPLVHH ENEEYKKVFF VLLSYIRKLY QELSQNMLMD YSFVMDIDKG
4860 4870 4880 4890 4900
SKFWEQEFYE NMYRAPTTLQ SCGVCVVCNS QTILRCGNCI RKPFLCCKCC
4910 4920 4930 4940 4950
YDHVMHTDHK NVLSINPYIC SQPGCGEADV TKLYLGGMSY FCGNHKPKLS
4960 4970 4980 4990 5000
IPLVSNGTVF GIYRANCAGS ENVDDFNQLA TTNWSTVEPY ILANRCVDSL
5010 5020 5030 5040 5050
RRFAAETVKA TEELHKQQFA SAEVREVLSD RELILSWEPG KTRPPLNRNY
5060 5070 5080 5090 5100
VFTGFHFTRT SKVQLGDFTF EKGEGKDVVY YRATSTAKLS VGDIFVLTSH
5110 5120 5130 5140 5150
NVVSLIAPTL CPQQTFSRFV NLRPNVMVPA CFVNNIPLYH LVGKQKRTTV
5160 5170 5180 5190 5200
QGPPGSGKSH FAIGLAAYFS NARVVFTACS HAAVDALCEK AFKFLKVDDC
5210 5220 5230 5240 5250
TRIVPQRTTI DCFSKFKAND TGKKYIFSTI NALPEVSCDI LLVDEVSMLT
5260 5270 5280 5290 5300
NYELSFINGK INYQYVVYVG DPAQLPAPRT LLNGSLSPKD YNVVTNLMVC
5310 5320 5330 5340 5350
VKPDIFLAKC YRCPKEIVDT VSTLVYDGKF IANNPESRQC FKVIVNNGNS
5360 5370 5380 5390 5400
DVGHESGSAY NITQLEFVKD FVCRNKEWRE ATFISPYNAM NQRAYRMLGL
5410 5420 5430 5440 5450
NVQTVDSSQG SEYDYVIFCV TADSQHALNI NRFNVALTRA KRGILVVMRQ
5460 5470 5480 5490 5500
RDELYSALKF IELDSVASLQ GTGLFKICNK EFSGVHPAYA VTTKALAATY
5510 5520 5530 5540 5550
KVNDELAALV NVEAGSEITY KHLISLLGFK MSVNVEGCHN MFITRDEAIR
5560 5570 5580 5590 5600
NVRGWVGFDV EATHACGTNI GTNLPFQVGF STGADFVVTP EGLVDTSIGN
5610 5620 5630 5640 5650
NFEPVNSKAP PGEQFNHLRA LFKSAKPWHV VRPRIVQMLA DNLCNVSDCV
5660 5670 5680 5690 5700
VFVTWCHGLE LTTLRYFVKI GKDQVCSCGS RATTFNSHTQ AYACWKHCLG
5710 5720 5730 5740 5750
FDFVYNPLLV DIQQWGYSGN LQFNHDLHCN VHGHAHVASA DAIMTRCLAI
5760 5770 5780 5790 5800
NNAFCQDVNW DLTYPHIANE DEVNSSCRYL QRMYLNACVD ALKVNVVYDI
5810 5820 5830 5840 5850
GNPKGIKCVR RGDLNFRFYD KNPIVPNVKQ FEYDYNQHKD KFADGLCMFW
5860 5870 5880 5890 5900
NCNVDCYPDN SLVCRYDTRN LSVFNLPGCN GGSLYVNKHA FHTPKFDRTS
5910 5920 5930 5940 5950
FRNLKAMPFF FYDSSPCETI QLDGVAQDLV SLATKDCITK CNIGGAVCKK
5960 5970 5980 5990 6000
HAQMYADFVT SYNAAVTAGF TFWVTNNFNP YNLWKSFSAL QSIDNIAYNM
6010 6020 6030 6040 6050
YKGGHYDAIA GEMPTIVTGD KVFVIDQGVE KAVFFNQTIL PTSVAFELYA
6060 6070 6080 6090 6100
KRNIRTLPNN RILKGLGVDV TNGFVIWDYT NQTPLYRNTV KVCAYTDIEP
6110 6120 6130 6140 6150
NGLIVLYDDR YGDYQSFLAA DNAVLVSTQC YKRYSYVEIP SNLLVQNGIP
6160 6170 6180 6190 6200
LKDGANLYVY KRVNGAFVTL PNTLNTQGRS YETFEPRSDV ERDFLDMSEE
6210 6220 6230 6240 6250
SFVEKYGKEL GLQHILYGEV DKPQLGGLHT VIGMCRLLRA NKLNAKSVTN
6260 6270 6280 6290 6300
SDSDVMQNYF VLADNGSYKQ VCTVVDLLLD DFLELLRNIL KEYGTNKSKV
6310 6320 6330 6340 6350
VTVSIDYHSI NFMAWFEDGI IKTCYPQLQS AWTCGYNMPE LYKVQNCVME
6360 6370 6380 6390 6400
PCNIPNYGVG IALPSGIMMN VAKYTQLCQY LSKTTMCVPH NMRVMHFGAG
6410 6420 6430 6440 6450
SDKGVAPGST VLKQWLPEGT LLVDNDIVDY VSDAHVSVLS DCNKYKTEHK
6460 6470 6480 6490 6500
FDLVISDMYT DNDSKRKHEG VIANNGNDDV FIYLSSFLRN NLALGGSFAV
6510 6520 6530 6540 6550
KVTETSWHEV LYDIAQDCAW WTMFCTAVNA SSSEAFLVGV NYLGASEKVK
6560 6570 6580 6590 6600
VSGKTLHANY IFWRNCNYLQ TSAYSIFDVA KFDLRLKATP VVNLKTEQKT
6610 6620 6630
DLVFNLIKCG KLLVRDVGNT SFTSDSFVCT M
Note: Produced by -1 ribosomal frameshifting at the 1a-1b genes boundary.
Length:6,631
Mass (Da):744,412
Last modified:June 10, 2008 - v1
Checksum:iCB222611D8C1B9E2
GO
Isoform Replicase polyprotein 1a (identifier: P0C6V5-1) [UniParc]FASTAAdd to basket

Also known as: pp1a, ORF1a polyprotein

The sequence of this isoform can be found in the external entry P0C6V5.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:3,953
Mass (Da):441,177
GO

Sequence cautioni

The sequence AAW33784.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence AAW33785.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence ABI26421.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence ABI26422.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti807 – 8071L → S.
Natural varianti1618 – 16181S → F.
Natural varianti1739 – 17391S → A.
Natural varianti2631 – 26311M → L.
Natural varianti2774 – 27741S → P.
Natural varianti4230 – 42301D → G.
Natural varianti4692 – 46921S → P.
Natural varianti4859 – 48591Y → C.
Natural varianti5104 – 51041S → P.
Natural varianti6033 – 60331V → A.
Natural varianti6080 – 60801T → M.
Natural varianti6314 – 63141A → T.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ834384 Genomic RNA. Translation: ABI26421.1. Sequence problems.
DQ834384 Genomic RNA. Translation: ABI26422.1. Sequence problems.
AY851295 Genomic RNA. Translation: AAW33784.1. Sequence problems.
AY851295 Genomic RNA. Translation: AAW33785.1. Sequence problems.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ834384 Genomic RNA. Translation: ABI26421.1. Sequence problems.
DQ834384 Genomic RNA. Translation: ABI26422.1. Sequence problems.
AY851295 Genomic RNA. Translation: AAW33784.1. Sequence problems.
AY851295 Genomic RNA. Translation: AAW33785.1. Sequence problems.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q6DX-ray2.35A/B/C2783-3088[»]
2Q6FX-ray2.00A/B2783-3088[»]
ProteinModelPortaliP0C6Y3.
SMRiP0C6Y3. Positions 2787-3088, 3799-3920.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC30.002.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP0C6Y3.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR032505. Corona_NSP4_C.
IPR009461. Coronavirus_NSP16.
IPR027352. CV_MBD_dom.
IPR002589. Macro_dom.
IPR009466. NSP11.
IPR014828. NSP7.
IPR014829. NSP8.
IPR014822. NSP9.
IPR027417. P-loop_NTPase.
IPR008740. Peptidase_C30.
IPR013016. Peptidase_C30/C16.
IPR009003. Peptidase_S1_PA.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009469. RNA_pol_N_coronovir.
IPR018995. RNA_synth_NSP10_coronavirus.
IPR029063. SAM-dependent_MTases.
IPR014827. Viral_protease.
[Graphical view]
PfamiPF16348. Corona_NSP4_C. 1 hit.
PF06478. Corona_RPol_N. 1 hit.
PF01661. Macro. 1 hit.
PF09401. NSP10. 1 hit.
PF06471. NSP11. 1 hit.
PF06460. NSP13. 1 hit.
PF08716. nsp7. 1 hit.
PF08717. nsp8. 1 hit.
PF08710. nsp9. 1 hit.
PF05409. Peptidase_C30. 1 hit.
PF00680. RdRP_1. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF08715. Viral_protease. 1 hit.
[Graphical view]
SMARTiSM00506. A1pp. 1 hit.
[Graphical view]
SUPFAMiSSF101816. SSF101816. 1 hit.
SSF144246. SSF144246. 1 hit.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51653. CV_MBD. 1 hit.
PS51442. M_PRO. 1 hit.
PS51154. MACRO. 1 hit.
PS51124. PEPTIDASE_C16. 1 hit.
PS51657. PSRV_HELICASE. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Avian infectious bronchitis virus strain M41."
    Mondal S.P., Buckles E.L.
    Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens."
    Callison S.A., Hilt D.A., Boynton T.O., Sample B.F., Robison R., Swayne D.E., Jackwood M.W.
    J. Virol. Methods 138:60-65(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiR1AB_IBVM
AccessioniPrimary (citable) accession number: P0C6Y3
Secondary accession number(s): Q0GNB9
, Q0GNC0, Q5I5Y0, Q5I5Y1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 10, 2008
Last modified: May 11, 2016
This is version 66 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete 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.