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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 :  03 Aug 15  (Deposition) - 28 Oct 15  (Release) - 02 Dec 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A,B,C,D,m,t
Keywords :  Dsrna Genome Organization, Viral Polymerase, Transferase-Viral Protein-Rna 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 - CPV 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
 
Molecule 4 - RNA (5'-R(P*GP*GP*GP*GP*GP*G)-3')
    Chains: t
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829
    Other Details: GENOMIC RNA
 
Molecule 5 - RNA (5'-R(P*CP*CP*CP*CP*C)-3')
    Chains: m
    Organism Common: BMCPV
    Organism Scientific: BOMBYX MORI CYPOVIRUS 1
    Organism Taxid: 110829
    Other Details: GENOMIC RNA

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDmt

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , ARG A:147 , TYR A:184 , PRO A:187BINDING SITE FOR RESIDUE GTP A 1301
2AC2SOFTWAREARG A:479 , ARG A:487 , ILE A:489 , VAL A:548 , ALA A:549 , GLY A:550 , ASP A:552 , SER A:639 , THR A:644 , HIS A:648 , ASP A:680 , C m:5 , G t:0 , G t:1BINDING SITE FOR RESIDUE CTP A 1302
3AC3SOFTWARELYS B:355 , GLY B:356 , GLY B:358 , LYS B:359 , THR B:360 , SER B:361 , ARG B:520 , GLN B:521 , ARG B:522BINDING SITE FOR RESIDUE GTP B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JB7)

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Thr A:5 -Lys A:6
2Lys A:239 -Asp A:240
3Ser A:425 -Pro A:426
4Lys A:435 -Leu A:436
5Leu A:436 -Glu A:437
6Val A:438 -Gly A:439
7Gly A:439 -Gly A:440
8Gly A:580 -Pro A:581
9Ser A:639 -Gly A:640
10Thr A:644 -Ser A:645
11Leu A:678 -Gly A:679
12Gly A:679 -Asp A:680
13Glu A:945 -Arg A:946
14Ile A:958 -Arg A:959
15Arg A:959 -Gly A:960
16Ser A:964 -Asn A:965
17Met A:982 -Ala A:983
18Ile B:303 -Pro B:304
19Ala B:499 -Arg B:500

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JB7)

(-) Exons   (0, 0)

(no "Exon" information available for 3JB7)

(-) 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:1198
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........eeeee.....eeeee...hhhhhh....hhhhh.....................hhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.......eeee....eeee.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhheeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhh...........eeeee.....eeeee...hhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh................hhhhhhh..hhhhhhhh......hhhhhhhh.....eeee.......eeee..hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..eeee..ee.......hhhhhhhhhhhhhhhhhhh..........eeeeeee......eeeeehhhhhhhhhhhhh.....eeee...eeee.............hhhhhhhhhhhhhhhhhhhhhh........eee....eeeeee.hhhhhhhhhhhhhhhhhhh...ee......ee......ee..ee...................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh......eee..hhhhhhhhhh....eee........eeeeee..hhhhhh............................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhh...........hhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhh........hhhhhhhhheeee........hhhhhhh....hhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..........................hhhhhhh.ee.hhhhh....hhhhhhhhhhhhhhhh........eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jb7 A    5 TKLHNTIFSETRKFTRESFKEIEHLTARLANDRVARHDFLFNTSIVLISDYSGEDSNGNQLQATITIPNEIINPKEYDPSDYPLAEDESFFKQGHKYDYLVTFRAGSLTNTYEPKTKMYKLHAALDKLMHVKQRKSRFADLWRELCAVIASLDVWYQTTNYPLRTYVKLLFHKGDEFPFYESPSQDRIIFNDKSVASILPTFVYTCCQVGTAIMSGILTHVESIVAMNHFLHCAKDSYIDEKLKIKGIGRSWYQEALHNVCQATVPVWSQFNEVIGHRTKSTSEPHFVSSTFISLRAKRAELLYPEFNAYINRAIQLSKTQNDVANYYAACRAMTNDGTFLATLTELSLDAAVFPRIEQHLVTRPAVLMSNTRHESLKQKYTNGVGSIAQSYLSSFTDEIAKRVNGRHHDEAWLNFLTTSSPGRKLTEIEKLEVGGDVAAWSNSRIVMQAVFAREYRTPERIFKSLKAPIKLVERQQSDRRQRAISGLDNDRLFLSFMPYTIGKQIYELNDNAAQGKQAGNAFDIGEMLYWTSQRNVLLSSIDVAGMDASVTTNTKDIYNTFVLDVASKCTVPRFGPYYAKNMEVFEAGNRQSQVRYVNAAWQACALEAANSQTSTSYESEIFGQVKNAEGTYPSGRADTSTHHTVLLQGLVRGNELKRASDGKNSCLATIKILGDDIMEIFQGSESDTYDHAVSNASILNESGFATTAELSQNSIVLLQQLVVNGTFWGFADRISLWTREDTKDIGRLNLAMMELNALIDDLVFRVRRPEGLKMLGFFCGAICLRRFTLSVDNKLYDSTYNNLSKYMTLTKYDKNPDSDSTLMSLILPLAWLFMPRGGEYPAYPFERRDGTFTEDESMFTARGAYKRRLLYDVSNIGEMIQQNSMALDDDLLHEYGFTGALLLIDLNILDLIDEVKKEDISPVKVSELATSLEQLGKLGEREKSRRAASDLKIRGHALSNDIVYGYGLQEKIQKSAMATKETTVQSKRVSSRLHDVIVAKRDYKISTIPADALHLHEFEVEDVTVDLLPHAKHTSYSSLAYNMSFGSDGWFAFALLGGLDRSANLLRLDVASIRGPVFKQGYKIYKSDATLLNDFFTAISAGPKEQGILLRAFAYYSLYGNVEYHYVLSPRQLFFLSDNPVSAERLVRIPPKYYVSTQCRALYNIFSYLHILRSIANNRGKRLKMVLHPGLIAYVRG 1211
                                    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       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074     |1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            1080|                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             1090                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhhhhh.........eee.hhhhhhh.hhhhhhhhh....eee..........hhhhhhhh.eeeee.................eeeee....hhhhhhhhhhhhhh......eeeeeee....ee.eee.................hhhhhhhheee.............eeeeeee.....hhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.......hhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......eeeee.hhhhhh.......eeee....hhhhhhhhh...hhhhhhhhhhhhh.......eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3jb7 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
                3jb7 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
                3jb7 D  111 PTVVQSRTDVFNEQFA  126
                                   120      


Chain m from PDB  Type:RNA  Length:5
                                      
                3jb7 m    1 CCCCC    5


Chain t from PDB  Type:RNA  Length:6
                                       
                3jb7 t    0 GGGGGG    5
   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 3JB7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JB7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly A:439 - Gly A:440   [ RasMol ]  
    Gly A:580 - Pro A:581   [ RasMol ]  
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    Leu A:678 - Gly A:679   [ RasMol ]  
    Lys A:239 - Asp A:240   [ RasMol ]  
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    Met A:982 - Ala A:983   [ RasMol ]  
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    Val A:438 - Gly A:439   [ 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: 3jb6
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(-) Related Entries Specified in the PDB File

3jb6