5MHJ

ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.

Tunnicliffe, R.B.Lockhart-Cairns, M.P.Levy, C.Mould, A.P.Jowitt, T.A.Sito, H.Baldock, C.Sandri-Goldin, R.M.Golovanov, A.P.

(2017) Nucleic Acids Res 45: 8064-8078

  • DOI: 10.1093/nar/gkx419
  • Primary Citation of Related Structures:  
    5MHK, 5MHJ

  • PubMed Abstract: 
  • The transcription factor ICP4 from herpes simplex virus has a central role in regulating the gene expression cascade which controls viral infection. Here we present the crystal structure of the functionally essential ICP4 DNA binding domain in comple ...

    The transcription factor ICP4 from herpes simplex virus has a central role in regulating the gene expression cascade which controls viral infection. Here we present the crystal structure of the functionally essential ICP4 DNA binding domain in complex with a segment from its own promoter, revealing a novel homo-dimeric fold. We also studied the complex in solution by small angle X-Ray scattering, nuclear magnetic resonance and surface-plasmon resonance which indicated that, in addition to the globular domain, a flanking intrinsically disordered region also recognizes DNA. Together the data provides a rationale for the bi-partite nature of the ICP4 DNA recognition consensus sequence as the globular and disordered regions bind synergistically to adjacent DNA motifs. Therefore in common with its eukaryotic host, the viral transcription factor ICP4 utilizes disordered regions to enhance the affinity and tune the specificity of DNA interactions in tandem with a globular domain.


    Organizational Affiliation

    Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major viral transcription factor ICP4AB201Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: ICP4IE175RS1
Find proteins for P08392 (Human herpesvirus 1 (strain 17))
Explore P08392 
Go to UniProtKB:  P08392
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')E12Human alphaherpesvirus 1
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')F12Human alphaherpesvirus 1
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ACY
      Query on ACY

      Download Ideal Coordinates CCD File 
      A, B
      ACETIC ACID
      C2 H4 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

      Download Ideal Coordinates CCD File 
      A
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.12 Å
      • R-Value Free: 0.235 
      • R-Value Work: 0.197 
      • R-Value Observed: 0.199 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 127.254α = 90
      b = 39.084β = 90
      c = 90.443γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      xia2data reduction
      xia2data scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of HealthUnited StatesAI107803

      Revision History 

      • Version 1.0: 2017-05-24
        Type: Initial release
      • Version 1.1: 2017-09-06
        Changes: Database references
      • Version 1.2: 2019-04-10
        Changes: Data collection, Source and taxonomy