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(-) Description

Title :  ICP4 DNA-BINDING DOMAIN, LACKING INTRINSICALLY DISORDERED REGION, IN COMPLEX WITH 12MER DNA DUPLEX FROM ITS OWN PROMOTER
 
Authors :  R. B. Tunnicliffe, M. P. Lockhart-Cairns, C. Levy, P. Mould, T. A. Jowit C. Baldock, R. M. Sandri-Goldin, A. P. Golovanov
Date :  24 Nov 16  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Transcription Factor, Dimer, Herpes, Virus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. Tunnicliffe, M. P. Lockhart-Cairns, C. Levy, A. P. Mould, T. A. Jowitt, H. Sito, C. Baldock, R. M. Sandri-Goldin, A. P. Golovanov
The Herpes Viral Transcription Factor Icp4 Forms A Novel Dn Recognition Complex.
Nucleic Acids Res. 2017
PubMed-ID: 28505309  |  Reference-DOI: 10.1093/NAR/GKX419

(-) Compounds

Molecule 1 - MAJOR VIRAL TRANSCRIPTION FACTOR ICP4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: T7 EXPRESS LYSY
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN, UNP RESIDUES 288-487
    Gene: ICP4, IE175, RS1
    Organism Common: HHV-1
    Organism Scientific: HUMAN HERPESVIRUS 1 (STRAIN 17)
    Organism Taxid: 10299
    Other Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 288-487
    Strain: 17
    Synonym: ALPHA-4 PROTEIN,INFECTED CELL PROTEIN 4,TRANSCRIPTIONAL ACTIVATOR IE175
 
Molecule 2 - DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: SYNTHETIC DNA, SEQUENCES MATCHES A REGION FROM THE ICP4 PROMOTER (IE3)
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')
    Chains: F
    Engineered: YES
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: SYNTHETIC DNA, SEQUENCES MATCHES A REGION FROM THE ICP4 PROMOTER (IE3)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:374 , ARG A:440 , TRP A:443 , ASN A:482binding site for residue ACY A 501
2AC2SOFTWAREARG A:305 , ARG A:472 , SER B:312binding site for residue CL A 502
3AC3SOFTWARETHR A:298 , ALA B:374 , THR B:377 , ARG B:440 , TRP B:443 , ASN B:482 , HOH B:616binding site for residue ACY B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MHJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5MHJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MHJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MHJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5MHJ)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....................eee......eee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mhj A 293 LDADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAALT 486
                                   302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    


Chain B from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...................eee......eee....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mhj B 294 DADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAALTG 487
                                   303       313       323       333       343       353       363       373       383       393       403       420       430       440       450       460       470       480       
                                                                                                                                               411|                                                                    
                                                                                                                                                419                                                                    


Chain E from PDB  Type:DNA  Length:9
                                         
                 5mhj E   2 CGATCGTCC  10


Chain F from PDB  Type:DNA  Length:9
                                         
                 5mhj F  31 GACGATCGG  39
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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 5MHJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MHJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MHJ)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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