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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FULL-LENGTH JAPANESE ENCEPHALITIS VIRUS NS5
 
Authors :  G. Lu, P. Gong
Date :  16 Apr 13  (Deposition) - 28 Aug 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, Rna-Dependent Rna Polymerase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Lu, P. Gong
Crystal Structure Of The Full-Length Japanese Encephalitis Virus Ns5 Reveals A Conserved Methyltransferase-Polymerase Interface
Plos Pathog. V. 9 03549 2013
PubMed-ID: 23950717  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003549

(-) Compounds

Molecule 1 - POLYPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2528-3432
    Gene: NS5
    Organism Scientific: JAPANESE ENCEPHALITIS VIRUS
    Organism Taxid: 11072
    Strain: AT31

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO418Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO410Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO48Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:85 , GLY A:86 , TRP A:87 , THR A:104 , LYS A:105 , HIS A:110 , VAL A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , SO4 A:1011 , HOH A:1145 , HOH A:1209BINDING SITE FOR RESIDUE SAH A 1001
02AC2SOFTWAREARG A:41 , ARG A:45 , HOH A:1116 , HOH A:1192 , THR B:38 , ARG B:41 , HOH B:1219BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWAREARG A:28 , ARG A:41 , ARG A:57 , ARG A:213 , ARG B:45BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREARG A:37 , ARG A:41 , ARG A:44 , ARG A:84 , HOH A:1142BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREALA A:31 , ARG A:243 , ARG A:246BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWAREARG A:28 , SER A:215 , ASN A:216BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWAREALA A:410 , LEU A:411 , GLY A:412 , HOH A:1153BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWAREARG A:734 , ARG A:742 , SER A:799 , TRP A:800 , SER A:801BINDING SITE FOR RESIDUE SO4 A 1008
09AC9SOFTWAREARG A:474 , GLY A:539 , LYS A:694BINDING SITE FOR RESIDUE SO4 A 1009
10BC1SOFTWAREGLY A:561 , ARG A:564 , GLN B:635 , HIS B:636 , LYS B:643BINDING SITE FOR RESIDUE SO4 A 1010
11BC2SOFTWAREGLY A:109 , HIS A:110 , GLU A:111 , SAH A:1001BINDING SITE FOR RESIDUE SO4 A 1011
12BC3SOFTWAREGLU A:440 , HIS A:444 , CYS A:449 , CYS A:452BINDING SITE FOR RESIDUE ZN A 1012
13BC4SOFTWAREHIS A:717 , CYS A:733 , GLU A:848 , CYS A:852BINDING SITE FOR RESIDUE ZN A 1013
14BC5SOFTWARESER B:56 , GLY B:58 , GLY B:81 , CYS B:82 , GLY B:85 , GLY B:86 , TRP B:87 , THR B:104 , LYS B:105 , HIS B:110 , VAL B:130 , ASP B:131 , VAL B:132 , PHE B:133 , ASP B:146 , ILE B:147 , SO4 B:1009 , HOH B:1125 , HOH B:1162 , HOH B:1252BINDING SITE FOR RESIDUE SAH B 1001
15BC6SOFTWAREARG A:42 , ARG A:45 , ARG B:28 , ARG B:41 , ARG B:57 , ARG B:213BINDING SITE FOR RESIDUE SO4 B 1002
16BC7SOFTWAREARG B:37 , ARG B:41 , ARG B:84 , HOH B:1215BINDING SITE FOR RESIDUE SO4 B 1003
17BC8SOFTWAREALA B:31 , ARG B:243 , ARG B:246BINDING SITE FOR RESIDUE SO4 B 1004
18BC9SOFTWAREARG B:28 , SER B:215 , ASN B:216BINDING SITE FOR RESIDUE SO4 B 1005
19CC1SOFTWAREALA B:410 , LEU B:411 , GLY B:412BINDING SITE FOR RESIDUE SO4 B 1006
20CC2SOFTWAREARG B:734 , SER B:799 , TRP B:800 , SER B:801BINDING SITE FOR RESIDUE SO4 B 1007
21CC3SOFTWAREARG B:474 , GLY B:539 , LYS B:694BINDING SITE FOR RESIDUE SO4 B 1008
22CC4SOFTWAREGLY B:109 , HIS B:110 , GLU B:111 , SAH B:1001BINDING SITE FOR RESIDUE SO4 B 1009
23CC5SOFTWAREHIS B:717 , CYS B:733 , GLU B:848 , CYS B:852BINDING SITE FOR RESIDUE ZN B 1010
24CC6SOFTWAREGLU B:440 , HIS B:444 , CYS B:449 , CYS B:452BINDING SITE FOR RESIDUE ZN B 1011

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K6M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K6M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K6M)

(-) Exons   (0, 0)

(no "Exon" information available for 4K6M)

(-) 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:888
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhhhhh....eee.hhhhhhhhhh..........hhhhhhhhhhh.......eeeeee....hhhhhhhhh...eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhhh........eee.................hhhhhhhhhhhhhhh...............eeeeeeee........eehhhhhhhhhhhhhhhhhhheee...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...eee..........eeee.hhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhh.eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhh.eeee..eeee.....hhhhhhhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6m A   5 GRTLGEQWKEKLNAMSREEFFKYRREAIIEVDRTEARRARRENNIVGGHPVSRGSAKLRWLVEKGFVSPIGKVIDLGCGRGGWSYYAATLKKVQEVRGYTKGGAGHEEPMLMQSYGWNLVSLKSGVDVFYKPSEPSDTLFCDIGESSPSPEVEEQRTLRVLEMTSDWLHRGPREFCIKVLCPYMPKVIEKMEVLQRRFGGGLVRLPLSRNSNHEMYWVSGAAGNVVHAVNMTSQVLLGRMDRTVWRGPKYEEDVNLGSGTRAVGKGSNQEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGSASSLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGAKEVLNETTNWLWAYLSREKRPRLCTKEEFIKKVNSNAALGAVFAEQNQWSTAREAVDDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGAGWNVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPITSWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMTSLRRYE 895
                                    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     ||277       287       297       307       317       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        
                                                                                                                                                                                                                                                                                                   270|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                    274                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:888
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhh...eee.hhhhhhhhhh..........hhhhhhhhhhhh......eeeeee....hhhhhhhh....eeeeeee................hhh.eeee...hhhhh......eeee.......hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.eee...........eeee.....hhhhhhhhhhhhhhhh.........eee................hhhhhhhhhhhhhhhh...............eeeeeeee........eehhhhhhhhhhhhhhhhhhheee...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...eee..........eeeeehhhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhh.eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhh.hhhhhhh.................hhhhh.....eeeeee.....eeeeee.hhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........................hhhhhhhhhhh.............hhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k6m B   5 GRTLGEQWKEKLNAMSREEFFKYRREAIIEVDRTEARRARRENNIVGGHPVSRGSAKLRWLVEKGFVSPIGKVIDLGCGRGGWSYYAATLKKVQEVRGYTKGGAGHEEPMLMQSYGWNLVSLKSGVDVFYKPSEPSDTLFCDIGESSPSPEVEEQRTLRVLEMTSDWLHRGPREFCIKVLCPYMPKVIEKMEVLQRRFGGGLVRLPLSRNSNHEMYWVSGAAGNVVHAVNMTSQVLLGRMDRTVWRGPKYEEDVNLGSGTRAVGKGSNQEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGSASSLVNGVVKLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGAKEVLNETTNWLWAYLSREKRPRLCTKEEFIKKVNSNAALGAVFAEQNQWSTAREAVDDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIWFMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGKQGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRHKVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLMEAEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDDRFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGRSIVVPCRGQDELIGRARISPGAGWNVKDTACLAKAYAQMWLLLYFHRRDLRLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENEWMMDKTPITSWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRAVIGKENYVDYMTSLRRYE 895
                                    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     ||277       287       297       307       317       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        
                                                                                                                                                                                                                                                                                                   270|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                    274
   Legend:   → Mismatch (orange background)
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  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 4K6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K6M)

(-) Gene Ontology  (62, 107)

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 Related Entries

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        POLG_JAEV1 | P27395: 2z83 3p54 4hdg 4hdh 4mtp
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(-) Related Entries Specified in the PDB File

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