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P29813 (POLG_EC11G) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 130. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 12 chains:

  1. Protein VP0
    Alternative name(s):
    VP4-VP2
  2. Protein VP4
    Alternative name(s):
    P1A
    Virion protein 4
  3. Protein VP2
    Alternative name(s):
    P1B
    Virion protein 2
  4. Protein VP3
    Alternative name(s):
    P1C
    Virion protein 3
  5. Protein VP1
    Alternative name(s):
    P1D
    Virion protein 1
  6. Protease 2A
    Short name=P2A
    EC=3.4.22.29
    Alternative name(s):
    Protein 2A
  7. Protein 2B
    Short name=P2B
  8. Protein 2C
    Short name=P2C
    EC=3.6.1.15
  9. Protein 3A
    Short name=P3A
  10. Protein 3B
    Short name=P3B
    Alternative name(s):
    VPg
  11. Protease 3C
    Short name=P3C
    EC=3.4.22.28
    Alternative name(s):
    Picornain 3C
  12. RNA-directed RNA polymerase 3D-POL
    Short name=P3D-POL
    EC=2.7.7.48
OrganismEchovirus 11 (strain Gregory) [Complete proteome]
Taxonomic identifier31705 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeEnterovirusEnterovirus B
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length2195 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor to provide virion attachment to target cell. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks By similarity.

Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome By similarity.

Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome By similarity.

Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks By similarity.

Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step By similarity.

Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut off the capped cellular mRNA transcription By similarity.

Protein 2B: Affects membrane integrity and cause an increase in membrane permeability By similarity.

Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities By similarity.

Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport By similarity.

Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease By similarity.

RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals By similarity.

Catalytic activity

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

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.

Subunit structure

Capsid proteins interact with host CD55.

Subcellular location

Protein VP2: Virion. Host cytoplasm Potential.

Protein VP3: Virion. Host cytoplasm Potential.

Protein VP1: Virion. Host cytoplasm Potential.

Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Protein 3B: Virion Potential.

Protease 3C: Host cytoplasm Potential.

RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Post-translational modification

Specific enzymatic cleavages in vivo by the viral proteases yield a variety of precursors and mature proteins. Polyprotein processing intermediates such as VP0 which is a VP4-VP2 precursor are produced. During virion maturation, non-infectious particles are rendered infectious following cleavage of VP0. This maturation cleavage is followed by a conformational change of the particle By similarity.

VPg is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity.

Myristoylation of VP4 is required during RNA encapsidation and formation of the mature virus particle By similarity.

Sequence similarities

Belongs to the picornaviruses polyprotein family.

Contains 2 peptidase C3 domains.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Ontologies

Keywords
   Biological processActivation of host autophagy by virus
Host gene expression shutoff by virus
Host translation shutoff by virus
Host-virus interaction
Inhibition of host innate immune response 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 entry into host cell
   Cellular componentCapsid protein
Host cytoplasm
Host cytoplasmic vesicle
Host membrane
Membrane
Virion
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
Ion channel
Nucleotidyltransferase
Protease
RNA-directed RNA polymerase
Thiol protease
Transferase
Viral ion channel
   PTMCovalent protein-RNA linkage
Lipoprotein
Myristate
Phosphoprotein
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processRNA-protein covalent cross-linking

Inferred from electronic annotation. Source: UniProtKB-KW

induction by virus of host autophagy

Inferred from electronic annotation. Source: UniProtKB-KW

ion transmembrane transport

Inferred from electronic annotation. Source: GOC

pore formation by virus in membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

pore-mediated entry of viral genome into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

protein oligomerization

Inferred from electronic annotation. Source: UniProtKB-KW

proteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host RIG-I activity

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host translation

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: InterPro

transcription, RNA-templated

Inferred from electronic annotation. Source: GOC

viral genome replication

Inferred from electronic annotation. Source: InterPro

virion attachment to host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componenthost cell cytoplasmic vesicle membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral to membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

membrane

Inferred from electronic annotation. Source: UniProtKB-KW

viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA helicase activity

Inferred from electronic annotation. Source: InterPro

RNA-directed RNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

cysteine-type endopeptidase activity

Inferred from electronic annotation. Source: InterPro

ion channel activity

Inferred from electronic annotation. Source: UniProtKB-KW

structural molecule activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 331330Protein VP0 Potential
PRO_0000311058
Chain2 – 6968Protein VP4 Potential
PRO_0000039703
Chain70 – 331262Protein VP2 Potential
PRO_0000039704
Chain332 – 569238Protein VP3 Potential
PRO_0000039705
Chain570 – 861292Protein VP1 Potential
PRO_0000039706
Chain862 – 1011150Protease 2A Potential
PRO_0000039707
Chain1012 – 111099Protein 2B Potential
PRO_0000039708
Chain1111 – 1439329Protein 2C Potential
PRO_0000039709
Chain1440 – 152889Protein 3A Potential
PRO_0000039710
Chain1529 – 155022Protein 3B Potential
PRO_0000039711
Chain1551 – 1733183Protease 3C Potential
PRO_0000039712
Chain1734 – 2195462RNA-directed RNA polymerase 3D-POL Potential
PRO_0000039713

Regions

Topological domain2 – 15051504Cytoplasmic Potential
Intramembrane1506 – 152116 Potential
Topological domain1522 – 2195674Cytoplasmic Potential
Domain1215 – 1371157SF3 helicase
Domain1960 – 2076117RdRp catalytic
Nucleotide binding1239 – 12468ATP Potential

Sites

Active site8821For protease 2A activity By similarity
Active site9001For protease 2A activity By similarity
Active site9711For protease 2A activity By similarity
Active site15901For protease 3C activity Potential
Active site16211For protease 3C activity Potential
Active site16971For protease 3C activity By similarity
Site69 – 702Cleavage Potential
Site331 – 3322Cleavage; by protease 3C Potential
Site861 – 8622Cleavage; by protease 2A Potential
Site1011 – 10122Cleavage; by protease 3C Potential
Site1110 – 11112Cleavage; by protease 3C Potential
Site1439 – 14402Cleavage; by protease 3C Potential
Site1528 – 15292Cleavage; by protease 3C Potential
Site1550 – 15512Cleavage; by protease 3C Potential
Site1733 – 17342Cleavage; by protease 3C Potential

Amino acid modifications

Modified residue15311O-(5'-phospho-RNA)-tyrosine By similarity
Lipidation21N-myristoyl glycine; by host By similarity

Experimental info

Sequence conflict823 – 8275RLCQY → SYANT in BAA01439. Ref.2

Secondary structure

................................................................................................................................................. 2195
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P29813 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 1CFC5DF288831AF0

FASTA2,195245,407
        10         20         30         40         50         60 
MGAQVSTQKT GAHETGLNAS GSSIIHYTNI NYYKDAASNS ANRQEFSQDP GKFTEPVKDI 

        70         80         90        100        110        120 
MVKSLPALNS PSAEECGYSD RVRSITLGNS TITTQESANV VVGYGRWPEY LKDNEATAED 

       130        140        150        160        170        180 
QPTQPDVATC RFYTLESVTW ERDSPGWWWK FPDALKDMGL FGQNMYYHYL GRAGYTLHVQ 

       190        200        210        220        230        240 
CNASKFHQGC LLVVCVPEAE MGCSQVDGTV NEHGLSEGET AKKFSSTSTN GTNTVQTIVT 

       250        260        270        280        290        300 
NAGMGVGVGN LTIYPHQWIN LRTNNCATIV MPYINNVPMD NMFRHHNFTL MIIPFVPLDY 

       310        320        330        340        350        360 
SSDSSTYVPI TVTVAPMCAE YNGLRLSTSL QGLPVMNTPG SNQFLTSDDF QSPSAMPQFD 

       370        380        390        400        410        420 
VTPELNIPGE VQNLMEIAEV DSVVPVNNVE GKLDTMEVYR IPVQSGNHQS DQVFGFQVQP 

       430        440        450        460        470        480 
GLDSVFKHTL LGEILNYFAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKNRKDAM 

       490        500        510        520        530        540 
LGTHIIWDVG LQSSCVLCVP WISQTHYRLV QQDEYTSAGN VTCWYQTGIV VPAGTPTSCS 

       550        560        570        580        590        600 
IMCFVSACND FSVRLLKDTP FIEQTALLQG DVVEAVENAV ARVADTIGSG PSNSQAVPAL 

       610        620        630        640        650        660 
TAVETGHTSQ VTPSDTMQTR HVKNYHSRSE SSIENFLSRS ACVYMGGYHT TNTDQTKLFA 

       670        680        690        700        710        720 
SWTISARRMV QMRRKLEIFT YVRFDVEVTF VITSKQDQGS RLGQDMPPLT HQIMYIPPGG 

       730        740        750        760        770        780 
PIPKSVTDYA WQTSTNPSIF WTEGNAPPRM SIPFISIGNA YSNFYDGWSH FSQNGVYGYN 

       790        800        810        820        830        840 
TLNHMGQIYV RHVNGSSPLP MTSTVRMYFK PKHVKAWVPR PPRLCQYKNA STVNFTPTNV 

       850        860        870        880        890        900 
TDKRTSINYI PETVKPDLSN YGAFGYQSGA VYVVNYRVVN RHLATHTDWQ NCVWEDYNRD 

       910        920        930        940        950        960 
LLISTTTAHG CDVIARCRCS TGVYYCQSKG KHYPVNFEGP GLVEVQESEY YPKRYQSHVL 

       970        980        990       1000       1010       1020 
LAAGFSEPGD CGGILRCEHG VIGIVTMGGE GVVGFADVRD LLWLEDDAME QGVKDYVEQL 

      1030       1040       1050       1060       1070       1080 
GNAFGSGFTN QICEQVNLLK ESLVGQDSIL EKSLKALVKI ISALVIVVRN HDDLITVTAT 

      1090       1100       1110       1120       1130       1140 
LALIGCTSSP WRWLKQKVSQ YYGIPMAERQ NNGWLKKFTE MTNSCKGMEW ISIKIQKFIE 

      1150       1160       1170       1180       1190       1200 
WLKVKILPEV REKHEFLNRL KQLPLLESQI ATIEQSAPSQ SDQEQLFSNV QYFAHYCRKY 

      1210       1220       1230       1240       1250       1260 
APLYASEAKR VFSLEKKMSN YIQFKSKCRI EPVCLLLHGS PGAGKSVATN LIGRSLAEKL 

      1270       1280       1290       1300       1310       1320 
NSSVYTLPPD PDHFDGYKQQ AVVIVDDLCQ NPDGKDVSLF CQMVSSVDFV PPMAALEEKG 

      1330       1340       1350       1360       1370       1380 
ILFTSLFVLA STNAGSINAP TVSDSRALAR RFHFDMNIEV ISMYSQNGKI NMPMSEKTCD 

      1390       1400       1410       1420       1430       1440 
EECCPVNFKR CCPLVCGKAI QFIDRRTQVR YSLDMLVTEM FREYNHRHSV GATLEALFQG 

      1450       1460       1470       1480       1490       1500 
PPIYREIKIS VAPETPPPPA IADLLKSVDS EAVREYCKEK GWLVPEVNST LQIEKHVSRA 

      1510       1520       1530       1540       1550       1560 
FICLQALTTF VSVAGIIYII YKLFAGFQGA YTGMPNQKPK VPTLRQAKVQ GPAFEFAVAM 

      1570       1580       1590       1600       1610       1620 
MKRNSSTVKT EYREFTMLGI YDRWAVLPRH AKPGPTILMN NQEVGVLDAK ELVDKDGTNL 

      1630       1640       1650       1660       1670       1680 
ELTLLKLNRN EKFRDIRGFL AKEEVEANQA VLAINTSKFP NMYIPVGQVT DYGFLNLGGT 

      1690       1700       1710       1720       1730       1740 
PTKRMLMSNF PTRAGQCGGV LMSTGKVLGI HVGGNGHQGF SAALLKHYFN DEQGEIEFIE 

      1750       1760       1770       1780       1790       1800 
SSKDAGFPII NTPSKTKLEP SVFHQVFEGD KEPAVLRNGD PRLKANFEEA IFSKYIGNVN 

      1810       1820       1830       1840       1850       1860 
THVDEYMLEA VDHYAGQLAT LDISTEPMRL EDAVYGTEGL EALDLTTSAG YPYVALGIKK 

      1870       1880       1890       1900       1910       1920 
RDILSRRTRD LTKLKECMDK YGLNLPMVTY VKDELRSADK VAKGKSRLIE ASSLNDSVAM 

      1930       1940       1950       1960       1970       1980 
RQTFGNLYRT FHLNPGIVTG SAVGCDPDLF WSKIPVMLDG HLIAFDYSGY DASLSPVWFA 

      1990       2000       2010       2020       2030       2040 
CLKLLLEKLG YTHKETNYID YLCNSHHLYR DKHYFERGGM PSGYSGTSMF NSMINNIIIR 

      2050       2060       2070       2080       2090       2100 
TLMLKVYKGI DLDQFRMIAY GDDVIASYPW PIDASLLAET GKGYGLIMTP ADKGECFNEV 

      2110       2120       2130       2140       2150       2160 
TWTNVTFLKR YFRADEQYPF LVHPVMPMKD IHESIRWTKD PKNTQDHVRS LCLLAWHNGE 

      2170       2180       2190 
HEYEEFIRKI RSVPVGRCLT LPAFSTLRRK WLDSF 

« Hide

References

[1]"The genome of echovirus 11."
Dahllund L., Nissinen L., Pulli T., Hyttinen V.P., Stanway G., Hyypiae T.
Virus Res. 35:215-222(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"Echoviruses include genetically distinct serotypes."
Auvinen P., Hyypiae T.
J. Gen. Virol. 71:2133-2139(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 822-2195.
[3]"Decay-accelerating factor (CD55), a glycosylphosphatidylinositol-anchored complement regulatory protein, is a receptor for several echoviruses."
Bergelson J.M., Chan M., Solomon K.R., St John N.F., Lin H., Finberg R.W.
Proc. Natl. Acad. Sci. U.S.A. 91:6245-6248(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HOST CD55.
[4]"Determination of the structure of a decay accelerating factor-binding clinical isolate of echovirus 11 allows mapping of mutants with altered receptor requirements for infection."
Stuart A.D., McKee T.A., Williams P.A., Harley C., Shen S., Stuart D.I., Brown T.D., Lea S.M.
J. Virol. 76:7694-7704(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 1-859.
Strain: Isolate clinical EV11-207.
+Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X80059 Genomic RNA. Translation: CAA56365.1.
D10582 Genomic RNA. Translation: BAA01439.1.
PIRGNNYEC. A36642.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2C8Ielectron microscopy14.00A570-857[»]
B79-328[»]
C332-569[»]
D2-69[»]
ProteinModelPortalP29813.
SMRP29813. Positions 2-69, 79-330, 332-858, 862-1011, 1551-2195.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC03.011.

Proteomic databases

PRIDEP29813.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D4.10.80.10. 2 hits.
InterProIPR003593. AAA+_ATPase.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR014838. P3A.
IPR000081. Peptidase_C3.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR003138. Pico_P1A.
IPR002527. Pico_P2B.
IPR001676. Picornavirus_capsid.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamPF08727. 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]
ProDomPD001306. Peptidase_C3. 1 hit.
PD649346. Pico_P2B. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 2 hits.
SSF52540. SSF52540. 1 hit.
SSF89043. SSF89043. 1 hit.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP29813.

Entry information

Entry namePOLG_EC11G
AccessionPrimary (citable) accession number: P29813
Secondary accession number(s): Q66785
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 130 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references