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: https://doi.org/10.1093/nar/gkx419
  • Primary Citation of Related Structures:  
    5MHJ, 5MHK

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major viral transcription factor ICP4
A, B
201Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: ICP4IE175RS1
UniProt
Find proteins for P08392 (Human herpesvirus 1 (strain 17))
Explore P08392 
Go to UniProtKB:  P08392
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08392
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')C [auth E]12Human alphaherpesvirus 1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')D [auth F]12Human alphaherpesvirus 1
Sequence Annotations
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  • Reference Sequence
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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesAI107803

Revision History  (Full details and data files)

  • 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