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(-) Description

Title :  CRYSTAL STRUCTURE OF VIRAL RDRP IN COMPLEX WITH GTP
 
Authors :  P. Surana, D. T. Nair
Date :  02 Oct 12  (Deposition) - 25 Dec 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Dna/Rna Polymerases, Rna Dependent Rna Polymerase, Gtp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Surana, V. Satchidanandam, D. T. Nair
Rna-Dependent Rna Polymerase Of Japanese Encephalitis Virus Binds The Initiator Nucleotide Gtp To Form A Mechanisticall Important Pre-Initiation State.
Nucleic Acids Res. V. 42 2758 2014
PubMed-ID: 24293643  |  Reference-DOI: 10.1093/NAR/GKT1106

(-) Compounds

Molecule 1 - POLYPROTEIN
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RNA DEPENDENT RNA POLYMERASE MODULE, RESIDUES 272-905
    Organism Scientific: JAPANESE ENCEPHALITIS VIRUS
    Organism Taxid: 11072
    Strain: P20778

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:463 , LYS A:471 , ARG A:474 , ASP A:541 , SER A:604 , ASP A:668 , ASP A:669 , ARG A:734 , ARG A:742 , SER A:799 , TRP A:800 , SER A:801 , HOH A:1260BINDING SITE FOR RESIDUE GTP A 1001
2AC2SOFTWAREGLU A:440 , HIS A:444 , CYS A:449 , CYS A:452BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREHIS A:717 , CYS A:733 , CYS A:852 , HOH A:1309BINDING SITE FOR RESIDUE ZN A 1003
4AC4SOFTWAREARG B:460 , LYS B:463 , LYS B:471 , ARG B:474 , ASP B:541 , SER B:604 , ASN B:613 , ASP B:668 , ASP B:669 , ARG B:734 , ARG B:742 , SER B:799 , TRP B:800 , SER B:801BINDING SITE FOR RESIDUE GTP B 1001
5AC5SOFTWAREGLU B:440 , HIS B:444 , CYS B:449 , CYS B:452BINDING SITE FOR RESIDUE ZN B 1002
6AC6SOFTWAREHIS B:717 , CYS B:733 , CYS B:852 , HOH B:1344BINDING SITE FOR RESIDUE ZN B 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HDG)

(-) Sequences/Alignments

Asymmetric 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:612
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...............eeeeeeee......hhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.............eeeee.hhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhh...........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hdg A 274 SNQEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLNETTNWLWAHLSREKRPRLCTKEEFIKKVNSNAALGAVFAEQNQWSTAREAVNDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGAGWNVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMT 889
                                   283       293       303       313   ||  327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887  
                                                                     317|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                      322                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:612
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...............eeeeeeee......hhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.............eeeee.hhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh.eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hdg B 274 SNQEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLNETTNWLWAHLSREKRPRLCTKEEFIKKVNSNAALGAVFAEQNQWSTAREAVNDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGAGWNVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMT 889
                                   283       293       303       313   ||  327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887  
                                                                     317|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                      322
   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 4HDG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (62, 107)

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 Related Entries

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        G3LHD9_9FLAV | G3LHD9: 4hdh 4mtp
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(-) Related Entries Specified in the PDB File

4hdh CRYSTAL STRUCTURE OF THE SAME VIRAL RDRP IN COMPLEX WITH ATP