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(-) Description

Title :  CRYSTAL STRUCTURE OF A PRODUCT STATE ASSEMBLY OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH BETA HAIRPIN DELETION BOUND TO PRIMER-TEMPLATE RNA WITH A 2',3'-DDC
 
Authors :  T. E. Edwards, R. T. Mosley
Date :  16 Mar 12  (Deposition) - 18 Apr 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Rdrp, Loopless Delta8, Ternary Complex, Product Complex, Flaviviridae, Hepatitis C Virus, Viral Protein, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Mosley, T. E. Edwards, E. Murakami, A. M. Lam, R. L. Grice, J. Du, M. J. Sofia, P. A. Furman, M. J. Otto
Structure Of Hepatitis C Virus Polymerase In Complex With Primer-Template Rna.
J. Virol. V. 86 6503 2012
PubMed-ID: 22496223  |  Reference-DOI: 10.1128/JVI.00386-12

(-) Compounds

Molecule 1 - 5'-R(*CP*AP*UP*GP*GP*C)-D(P*(DOC))-3'
    Chains: T, P
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - RNA-DIRECTED RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: VCID 5854
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Gene: NS5B
    Mutation: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 356411
    Strain: JFH-1
    Synonym: NS5B, P68

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DOC2Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4E7A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E7A)

(-) Exons   (0, 0)

(no "Exon" information available for 4E7A)

(-) 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    
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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:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eee..........................hhh.eee....hhhhhhhhhh.ee....hhhhhhhhhhhhhhhhh......hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eee...........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.....eeee..eeeeeee.hhhhhhhhhhhhhhhhhhhhh...........hhhhh.....eeeeee.....eeeeee..hhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7a A   0 SSMSYSWTGALITPCSPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLQQACQLTPPHSARSKYGFGAKEVRSLSGRAVNHIKSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESIYQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLGGVNPLDLPAIIERLHGLDAFSMHTYSHHELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEAR 543
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     ||457       467       477       487       497       507       517       527       537      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       445|                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        454                                                                                         


Chain P from PDB  Type:DNA/RNA  Length:5
                                     
                 4e7a P   3 UGGCc   7
                                |
                                7-DOC


Chain T from PDB  Type:DNA/RNA  Length:5
                                     
                 4e7a T   3 UGGCc   7
                                |
                                |
                                7-DOC
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  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 4E7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E7A)

(-) Gene Ontology  (92, 92)

Asymmetric/Biological Unit(hide GO term definitions)

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  4e7a
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  POLG_HCVJF | Q99IB8
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HCVJF | Q99IB8: 2kzq 2lif 2lvg 2xxd 2xym 3i5k 4aep 4aex 4e76 4e78 4j1v 4obc 4wt9 4wta 4wtc 4wtd 4wte 4wtf 4wtg 4wti 4wtj 4wtk 4wtl 4wtm 5twm 5uj2

(-) Related Entries Specified in the PDB File

4e76 NS5B APO STRUCTURE
4e78 NS5B BOUND TO PRIMER-TEMPLATE WITH 3'-DG