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Title :  THE COMPLEX CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF VIRF-1 FROM THE ONCOGENIC KSHV WITH DNA
 
Authors :  K. Hew, R. Venkatachalam
Date :  17 Oct 12  (Deposition) - 13 Mar 13  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (2x),D (2x)
Keywords :  Helix-Turn-Helix, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hew, S. L. Dahlroth, R. Venkatachalam, F. Nasertorabi, B. T. Lim, T. Cornvik, P. Nordlund
The Crystal Structure Of The Dna-Binding Domain Of Virf-1 From The Oncogenic Kshv Reveals A Conserved Fold For Dna Binding And Reinforces Its Role As A Transcription Factor.
Nucleic Acids Res. V. 41 4295 2013
PubMed-ID: 23435230  |  Reference-DOI: 10.1093/NAR/GKT082

(-) Compounds

Molecule 1 - K9
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21-DE3-ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN, UNP RESIDUES 88-196
    Gene: ORF K9, VIRF, VIRF-1
    Organism Common: HHV-8
    Organism Scientific: HUMAN HERPESVIRUS 8
    Organism Taxid: 37296
    Synonym: LATENT VIRAL INTERFERON REGULATORY FACTOR, LYTIC VIRAL INTERFERON REGULATORY FACTOR, ORF K9, VIRF-1 PROTEIN
 
Molecule 2 - 5'-D(*GP*CP*GP*TP*CP*GP*AP*GP*AP*CP*GP*C)-3'
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A (1x)B (1x)C (2x)D (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4HLY)

(-) Sites  (0, 0)

(no "Site" information available for 4HLY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HLY)

(-) Sequences/Alignments

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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....ee......eeeee.........hhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhh...eeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4hly A   3 KASIKDWIVCQVNSGKFPGVEWEDEERTRFRIPVTPLADPCFEWRRDGELGVVYIRERGNMPVDASFKGTRGRRRMLAALRRTRGLQEIGKGISQDGHHFLVFRVR 108
                                    12        22        32        42        52        62        72        82        92       102      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....ee......eeeee.........hhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4hly B   3 KASIKDWIVCQVNSGKFPGVEWEDEERTRFRIPVTPLADPCFEWRRDGELGVVYIRERGNMPVDASFKGTRGRRRMLAALRRTRGLQEIGKGISQDGHHFLVFRVR 108
                                    12        22        32        42        52        62        72        82        92       102      


Chain C from PDB  Type:DNA  Length:12
                                            
                 4hly C   1 GCGTCGAGACGC  12
                                    10  


Chain D from PDB  Type:DNA  Length:12
                                            
                 4hly D   1 GCGTCGAGACGC  12
                                    10
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4HLY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 14)

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  VIRF1_HHV8P | F5HF68
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 Related Entries

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

UniProtKB/Swiss-Prot
        VIRF1_HHV8P | F5HF68: 4ysi
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(-) Related Entries Specified in the PDB File

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