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(-) Description

Title :  IN SITU STRUCTURES OF THE SEGMENTED GENOME AND RNA POLYMERASE COMPLEX INSIDE A DSRNA VIRUS
 
Authors :  X. Zhang, K. Ding, X. K. Yu, W. Chang, J. C. Sun, Z. H. Zhou
Date :  02 Aug 15  (Deposition) - 28 Oct 15  (Release) - 02 Dec 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dsrna Genome Organization, Viral Polymerase, Transferase-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhang, K. Ding, X. Yu, W. Chang, J. Sun, Z. Hong Zhou
In Situ Structures Of The Segmented Genome And Rna Polymerase Complex Inside A Dsrna Virus.
Nature V. 527 531 2015
PubMed-ID: 26503045  |  Reference-DOI: 10.1038/NATURE15767

(-) Compounds

Molecule 1 - RNA-DEPENDENT RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.48
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829
 
Molecule 2 - VIRAL STRUCTURAL PROTEIN 4
    Chains: B
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829
 
Molecule 3 - VP1 CSP
    Chains: C, D
    Fragment: UNP RESIDUES 111-134
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:35 , ARG A:37 , ARG A:40 , ASP A:144 , ARG A:147 , TYR A:184 , ASN A:195 , ARG A:791BINDING SITE FOR RESIDUE GTP A 1301
2AC2SOFTWAREGLY B:356 , GLY B:358 , LYS B:359 , THR B:360 , SER B:361 , ASP B:384 , ASP B:412 , ARG B:520 , ARG B:522BINDING SITE FOR RESIDUE GTP B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JB6)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Thr A:5 -Lys A:6
2Lys A:239 -Asp A:240
3Gly A:580 -Pro A:581
4Ser A:879 -Asn A:880
5Gly A:1064 -Leu A:1065
6Ile B:303 -Pro B:304
7Ala B:499 -Arg B:500

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JB6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JB6)

(-) Exons   (0, 0)

(no "Exon" information available for 3JB6)

(-) 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 A from PDB  Type:PROTEIN  Length:1196
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeee.....eeeee...hhhhhh....hhhhh.................................hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......eeee....eeee.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh............hhhhhhh...........eeeeee....eeeee...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhh....eee.......eee.....hhhhhhhhhhhhhhhhhhh.................hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.eeeeeee......eeeeehhhhhhhhhhhhh.....eeee...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeeee.hhhhhhhhhhhhhhhhhhh......eee..eee...eeee....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh...eeee........eeeeeee.hhhhhhh...........................hhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhh........hhhhhhh...hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh...........eeehhhhhhhhhhhhhhh....hhhhhhh.eeeeeeeee....hhhhhh............hhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhh..................hhhhhhh.ee..hhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jb6 A    5 TKLHNTIFSETRKFTRESFKEIEHLTARLANDRVARHDFLFNTSIVLISDYSGEDSNGNQLQATITIPNEIINPKEYDPSDYPLAEDESFFKQGHKYDYLVTFRAGSLTNTYEPKTKMYKLHAALDKLMHVKQRKSRFADLWRELCAVIASLDVWYQTTNYPLRTYVKLLFHKGDEFPFYESPSQDRIIFNDKSVASILPTFVYTCCQVGTAIMSGILTHVESIVAMNHFLHCAKDSYIDEKLKIKGIGRSWYQEALHNVCQATVPVWSQFNEVIGHRTKSTSEPHFVSSTFISLRAKRAELLYPEFNAYINRAIQLSKTQNDVANYYAACRAMTNDGTFLATLTELSLDAAVFPRIEQHLVTRPAVLMSNTRHESLKQKYTNGVGSIAQSYLSSFTDEIAKRVNGRHHDEAWLNFLTTSRIVMQAVFAREYRTPERIFKSLKAPIKLVERQQSDRRQRAISGLDNDRLFLSFMPYTIGKQIYELNDNAAQGKQAGNAFDIGEMLYWTSQRNVLLSSIDVAGMDASVTTNTKDIYNTFVLDVASKCTVPRFGPYYAKNMEVFEAGNRQSQVRYVNAAWQACALEAANSQTSTSYESEIFGQVKNAEGTYPSGRADTSTHHTVLLQGLVRGNELKRASDGKNSCLATIKILGDDIMEIFQGSESDTYDHAVSNASILNESGFATTAELSQNSIVLLQQLVVNGTFWGFADRISLWTREDTKDIGRLNLAMMELNALIDDLVFRVRRPEGLKMLGFFCGAICLRRFTLSVDNKLYDSTYNNLSKYMTLTKYDKNPDSDSTLMSLILPLAWLFMPRGGEYPAYPFERRDGTFTEDESMFTARGAYKRRLLYDVSNIGEMIQQNSMALDDDLLHEYGFTGALLLIDLNILDLIDEVKKEDISPVKVSELATSLEQLGKLGEREKSRRAASDLKIRGHALSNDIVYGYGLQEKIQKSAMATKETTVQSKRVSSRLHDVIVAKTRDYKISTIPADALHLHEFEVEDVTVDLLPHAKHTSYSSLAYNMSFGSDGWFAFALLGGLDRSANLLRLDVASIRGNYHKFSYDDPVFKQGYKIYKSDATLLNDFFTAISAGPKEQGILLRAFAYYSLYGNVEYHYVLSPRQLFFLSDNPVSAERLVRIPPKYYVSTQCRALYNIFSYLHILRSIANNRGKRLKMVLHPGLIAYVRGTSQGAILPEADN 1224
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424|      458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      
                                                                                                                                                                                                                                                                                                                                                                                                                                                             424|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                              449                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..........hhhhhhhhhhhhhhh.......eee.hhhhhh..hhhhhhhhh....eee..........hhhhhhhh.eeeee.................eeeee....hhhhhhhhh...........eeeeee......eeeee.................hhhhhhhheee.............eeeeeee.......hhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhh.......hhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......eeeeee.hhhhhhh......eeee....hhhhhhhhh...hhhhhhhhhhhhhhh....eeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3jb6 B    2 FAIDPLKHSKLYEEYGLYLRPHAPTIRSIKYASLIHSMLAKHAARHNGTLINPRMYADMITLGNTKVTDIVTYKALTEMSTLIESFRLPSGLALIIFDDEKYQSLIPNYINQLIAYTQPHIIPTWQGIADFSDTYLRSYFKRPFELTASNLAAPQKYNLSPMTRSIFNNTGREDAVIRKLYGYGEYVFIRYEGCLITWTGIYGEVTMMVNLSKRDLGLDVGDDYLKEYKKLLFYGVITDAIPSGISARSTIMKISPHKMMNPSGGALAVLSKFLEAVVSTNVINATLVVYAEKGAGKTSFLSTYAEQLSLASGQVVGHLSSDAYGRWLAKNKDVEEPSFAYDYVLSLDTDDNESYYEQKASELLISHGISEVAQYELLSVRKKIKMMDEMNEVLIAQLENADTHSERNFYYMVSTGKTTPRTLIVEGHFNAQDATIARTDTTVLLRTINDTTQAMRDRQRGGVVQLFLRDTYYRLLPALHTTVYPFEMLESIRRWKWV  560
                                    11        21 ||     47        57        67        77       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        
                                                23|                                           85|                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                 40                                           131                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:21
                                                      
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                3jb6 C  114 VQSRTDVFNEQFANEALHPMT  134
                                   123       133 


Chain D from PDB  Type:PROTEIN  Length:16
                                                 
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                3jb6 D  111 PTVVQSRTDVFNEQFA  126
                                   120
   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 3JB6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JB6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JB6)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ala B:499 - Arg B:500   [ RasMol ]  
    Gly A:1064 - Leu A:1065   [ RasMol ]  
    Gly A:580 - Pro A:581   [ RasMol ]  
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    Lys A:239 - Asp A:240   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        D3JWE6_CPVBM | D3JWE6: 3iz3 3j17 5h0s
UniProtKB/TrEMBL
        D0EZK6_CPVBM | D0EZK6: 3jb7
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(-) Related Entries Specified in the PDB File

3jb7