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(-) Description

Title :  EM STRUCTURE OF VP1A AND VP1B
 
Authors :  X. Li, N. Zhou, B. Xu, W. Chen, B. Zhu, X. Wang, J. Wang, H. Liu, L. Cheng
Date :  06 Oct 16  (Deposition) - 25 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.30
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Structural Classification, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, N. Zhou, W. Chen, B. Zhu, X. Wang, B. Xu, J. Wang, H. Liu, L. Cheng
Near-Atomic Resolution Structure Determination Of A Cypovirus Capsid And Polymerase Complex Using Cryo-Em At 200Kv
J. Mol. Biol. V. 429 79 2017
PubMed-ID: 27914893  |  Reference-DOI: 10.1016/J.JMB.2016.11.025

(-) Compounds

Molecule 1 - VP1
    Chains: B, C
    Engineered: YES
    Expression System: CYPOVIRUS
    Expression System Taxid: 10981
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5H0S)

(-) Sites  (0, 0)

(no "Site" information available for 5H0S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H0S)

(-) Cis Peptide Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1Tyr B:199 -Gly B:200
2Gln B:229 -Asp B:230
3Ile B:235 -Gly B:236
4Pro B:442 -Val B:443
5Glu B:472 -Ala B:473
6Pro B:505 -Ser B:506
7Gly B:564 -Glu B:565
8Gly B:826 -Gly B:827
9Glu B:845 -Gly B:846
10Asp B:1082 -Asp B:1083
11Ala B:1282 -Asn B:1283
12Val B:1317 -Glu B:1318
13Asn B:1332 -Ala B:1333
14Thr C:875 -Gly C:876
15Ser C:1279 -Pro C:1280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H0S)

(-) Exons   (0, 0)

(no "Exon" information available for 5H0S)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain B from PDB  Type:PROTEIN  Length:1148
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................eeeeeee.......hhhhhhhhhhhhhhh...eeeeeeee.....hhhh.ee......ee.............hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhh.........eeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhheehhhhhhhhhh......ee.........ee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh.....hhhhhhhhhhh......ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.....ee........hhhhhh...ee.hhh......hhhhhhhhhh.....eeeehhhhhhhh........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eeee......ee.............eehhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeehhhhhhhhhhhhhhh............hhhhhhhhhhhh...ee......hhhhhhhhhhhh..eeee.............eeeeeeehhhhh........hhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh....eeeeee..eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee.................eee.....eeeee....eeeee..................eeee......hhhhhhhhhhhhhhhh.eeeeeeeeeeeeee............hhhhhh....eeeeeee...................eeeee..........ee........................................................eeeeee.............ee...hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5h0s B  134 TKVIFNGLDVNTEVQPLSDDFKQISDPKGYLTYSVKYEDQFTKASEADDRIVGPTVNLFKYGAAVVNIDLNRDFFDTATGIDLTKGIPLVQDLLVPIGVTAGAEQSAEYVSGLLMVLFKVMTDNRLVIVGETTTPMSNTLSTVVNNVLRTTYHNNVGVNPALLRDFTQVNWLNRDITNMLQQAGTKYGLGLTETRLDYVRLVKTIVGHALNIDHFAASVLNINLRALMEANVTADDRIKALQAHSMISTQFHGPNQGALRPELAFDHDHIIRCLMLAAANYPRLEGIIVQINTGYVASANVIRPVYFPENLEQNQSAARLVSAVKARASEADISSIHLAIAREVSPMFNVHELKKIAESFEDPSSIVVVLEFILFALFFPTEFNRIKGDIQNVLLLFFSRWYPVEYGIFIQRGATYTINAAGEFEFSGRNEKWDQSLYLSEHFPALFSDVPLAGANTIIAIMRLFTPQGFLRTDDLAIAANFPRASRNPQTYIPYTNQRGTVTNEFASRFRTIVATLANVVNERAVQDDMQKATRSCTKQWLRHLETQFDNIAVAHTDHLSVVYATMSNFMLNFTNNFSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVEIVYPDPSTTLSQSLSVAQVLSKLTLPDAFINMILSGGDSVVMRTYQTEGIRMTTYDQYLSHIRERLHITNVPDPIYITGASTPDQIAASVQATHVAVVLYQSGVINGSASTYLRENEVLVVMPDYYDVVSRNNNRYHESVLEIADIFDQADFIQTSDAVRQLRALMPTLSTSQIRHAIERIAQITDYGKLTLRFMQNAQIRRIRPDGTVLRYDDQIDIEAFRWSRYFLDELRLRRLSVGLRLITNPRIARRFDGVRIMYLTDDDPDPDFVPDVPEGYVAVQYAHRLFSSSLANKRNRVTYTHPPTGMAYPSPTGRPHVHMTINERAGMSKLVADNIIASVIKSNWVVDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMDGLLRPEPSAFDPPASGEDMRLIYPLQPISVARSMRAIVNHNEVDRPRGAVAPSSYEMDTGTLSRNGDLLYSPVANGQVGIPKLEVDHISFSNVVSMMTANIRTGDDMAVERVNPDDVRAINIRNA 1333
                                   143       153       163       173  ||   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438    || 452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772  ||   796       806       816       826       836||     853       863       873       883       893       903       913       923    || 941       951       961       971       981       996      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325        
                                                                    176|                                                                                                                                                                                                                                                                  443|                                                                                                                                                                                                                                                                                                                                    775|                                            837|                                                                                928|                                                  990|    1004|                                                                                                                                                                                                                                                                                                                               
                                                                     182                                                                                                                                                                                                                                                                   448                                                                                                                                                                                                                                                                                                                                     790                                             845                                                                                 937                                                   996     1014                                                                                                                                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:1247
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...............................................................ee................eeeeeeee............hhhhhh...........eeeeeeee.....hhhhh.........................hhhhhh...hhhhhhhh.............hhhhhhhhhhh......................hhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....ee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh.....hhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eee................ee.hhhh.....hhhhhhhhh.......eeehhhhhhh.........eee...........hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh............hhhhh....eeee.....eee...............hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.............eeeehhhhhhhhhhhhhh...............hhhhhhhhhh....ee......hhhhhhhhhh....eee.......................ee.................hhhhhhhhhh....hhhhhhhhhhhhhhh.........ee.....ee.........eeeeee...ee........hhhhh........hhhhhhhhhhhhhhh.........eeeeee..........................ee..........ee..............................hhhhhhhhhhhhh...........ee...........................ee.......................eeeee..........eee......................................................................ee.ee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5h0s C   73 AKIATASSARQTDVEKPADVTFTIENVDDVGIMQQKKPPTVVQSRTDVFNEQFANEALHPMTKVIFNGLDVNTEVQPLSDDFKQISDPKGYLTYSVKYEDQFTKKDKLRASEADDRIVGPTVNLFKYGAAVVNIDLNRDFFDTATGIDLTKGIPLVQDLLVPIGVTAGAEQSAEYVSGLLMVLFKVMTDNRLVIVGETTTPMSNTLSTVVNNVLRTTYHNNVGVNPALLRDFTQVNWLNRDITNMLQQAGTKYGLGLTETRLDYVRLVKTIVGHALNIDHFAASVLNINLRALMEANVTADDRIKALQAHSMISTQFHGPNQGALRPELAFDHDHIIRCLMLAAANYPRLEGIIVQINTGYVASANVIRPVSEKRYFPENLEQNQSAARLVSAVKARASEADISSIHLAIAREVSPMFNVHELKKIAESFEDPSSIVVVLEFILFALFFPTEFNRIKGDIQNVLLLFFSRWYPVEYGIFIQRGATYTINAAGEFEFSGRNEKWDQSLYLSEHFPALFSDVPLAGANTIIAIMRLFTPQGFLRTDDLAIAANFPRASRNPQTYIPYTNQRGTVTNEFASRFRTIVATLANVVNERAVQDDMQKATRSCTKQWLRHLETQFDNIAVAHTDHLSVVYATMSNFMLNFTNNFSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVEIVYPDPSTTLSQSLSVAQVLSKLTLPDAFINMILSGGDSVVMRTYQTEADDDLDEGIRMTTYDQYLSHIRERLHITNVPDPIYITGASTPDQIAASVQATHVAVVLYQSGVINGSASTYLRENEVLVVMPDYYDVVSRFANANLQMNNNRYHESVLEIADIFDQADFIQTSDAVRQLRALMPTLSTSQIRHAIERIAQITDVDSTDYGKLTLRFLGTLTRSLKMQNAQIRRIRPDGTVLRYDDQIDIEAFRWSRYFLDELRLRRLSVGLRLITNPRIARRFDGVRIMYLTDDDPDPDFVPDVPEGYVAVQYAHRLFSSSLANKRNRVTYTHPPTGMAYPSPTGRPHVHMTINERAGMSKLVADNIIASVIKSNWVVDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMDGLLRPEPSAFDPPASGEDMRLIYPLQPISVARSMRAIVNHNEVDRPRGAVAPSSYEMDTGTLSRNGDLLYSPVANGQVGIPKLEVDHISFSNVVSMMTANIRTGDDMAVERVNPDDVRAINIRNA 1333
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772  ||   796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        775|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         790
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5H0S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H0S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H0S)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5h0s)
 
  Sites
(no "Sites" information available for 5h0s)
 
  Cis Peptide Bonds
    Ala B:1282 - Asn B:1283   [ RasMol ]  
    Asn B:1332 - Ala B:1333   [ RasMol ]  
    Asp B:1082 - Asp B:1083   [ RasMol ]  
    Gln B:229 - Asp B:230   [ RasMol ]  
    Glu B:472 - Ala B:473   [ RasMol ]  
    Glu B:845 - Gly B:846   [ RasMol ]  
    Gly B:564 - Glu B:565   [ RasMol ]  
    Gly B:826 - Gly B:827   [ RasMol ]  
    Ile B:235 - Gly B:236   [ RasMol ]  
    Pro B:442 - Val B:443   [ RasMol ]  
    Pro B:505 - Ser B:506   [ RasMol ]  
    Ser C:1279 - Pro C:1280   [ RasMol ]  
    Thr C:875 - Gly C:876   [ RasMol ]  
    Tyr B:199 - Gly B:200   [ RasMol ]  
    Val B:1317 - Glu B:1318   [ RasMol ]  
 

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  D3JWE6_CPVBM | D3JWE6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CAPSD_CPVBM | Q6TS43: 3cnf 3iz3 3izx 3j17 3jay 3jaz 3jb0 3jb1 3jb2 3jb3
        D3JWE6_CPVBM | D3JWE6: 3iz3 3j17
UniProtKB/TrEMBL
        D3JWE6_CPVBM | D3JWE6: 3jb6 3jb7

(-) Related Entries Specified in the PDB File

5h0r