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(-) Description

Title :  CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS AND DELTA8 BETA HAIRPIN LOOP DELETION IN COMPLEX WITH SOFOSBUVIR DIPHOSPHATE GS-607596, MN2+ AND SYMMETRICAL PRIMER TEMPLATE 5'-CAAAAUUU
 
Authors :  T. E. Edwards, T. C. Appleby
Date :  30 Oct 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Hcv, Viral, Ns5B, Rdrp, Resistance Mutation, Template, Primer, Primed Initiation, Delta8 Beta Hairpin Loop Deletion, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. C. Appleby, J. K. Perry, E. Murakami, O. Barauskas, J. Feng, A. Cho, D. Fox, D. R. Wetmore, M. E. Mcgrath, A. S. Ray, M. J. Sofia, S. Swaminathan, T. E. Edwards
Structural Basis For Rna Replication By The Hepatitis C Virus Polymerase.
Science V. 347 771 2015
PubMed-ID: 25678663  |  Reference-DOI: 10.1126/SCIENCE.1259210

(-) Compounds

Molecule 1 - RNA PRIMER TEMPLATE CAAAAUUU
    ChainsT, P
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 2 - RNA-DIRECTED RNA POLYMERASE
    ChainsA
    EC Number2.7.7.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificHEPATITIS C VIRUS JFH-1
    Organism Taxid356411

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
16GS1Ligand/Ion2'-DEOXY-2'-FLUORO-2'-METHYLURIDINE 5'-(TRIHYDROGENDIPHOSPHATE)
2CL1Ligand/IonCHLORIDE ION
3MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:220 , ASP A:318 , ASP A:319 , MN A:601 , U P:6 , 6GS P:602 , HOH P:701binding site for residue MN P 601
2AC2SOFTWAREARG A:48 , LYS A:141 , ARG A:158 , ASP A:220 , THR A:221 , HIS A:223 , PHE A:224 , ASP A:225 , THR A:287 , ASN A:291 , ASP A:318 , MN A:601 , U P:6 , MN P:601 , HOH P:701 , HOH P:702 , A T:2 , A T:3binding site for residue 6GS P 602
3AC3SOFTWAREASP A:220 , THR A:221 , ASP A:318 , MN P:601 , 6GS P:602 , HOH P:702binding site for residue MN A 601
4AC4SOFTWAREGLU A:237 , HIS A:254binding site for residue MN A 602
5AC5SOFTWAREGLY A:375 , PRO A:376 , ARG A:377 , GLY A:378 , ARG A:379 , ARG A:381binding site for residue CL A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WTG)

(-) 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:535
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........................hhh.eee....hhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhhh...........hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhh.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wtg A   0 SSMSYSWTGALITPCGPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLQQACQLTPPHSARSKYGFGAKEVRSLSGRAVNHIKSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRHFDSTVTERDIRTEESIYQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLIVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLGGVNPLDLPAIIERLHGLDAFSMHTYSHHELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEA 542
                                     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:6
                                      
                 4wtg P   1 AAAUUU   6

Chain T from PDB  Type:DNA/RNA  Length:8
                                        
                 4wtg T   1 CAAAAUUU   8

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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 4WTG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (92, 92)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HCVJF | Q99IB82kzq 2lif 2lvg 2xxd 2xym 3i5k 4aep 4aex 4e76 4e78 4e7a 4j1v 4obc 4wt9 4wta 4wtc 4wtd 4wte 4wtf 4wti 4wtj 4wtk 4wtl 4wtm 5twm 5uj2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4WTG)