5MHK

ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RS1
A, C, D, B
231Human herpesvirus 1 (strain 17)Gene Names: ICP4 (IE175)
Find proteins for P08392 (Human herpesvirus 1 (strain 17))
Go to UniProtKB:  P08392
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ICP4 DNA BINDING DOMAIN
J
4Human herpesvirus 1 (strain 17)Gene Names: ICP4 (IE175)
Find proteins for P08392 (Human herpesvirus 1 (strain 17))
Go to UniProtKB:  P08392
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')G,E19Human alphaherpesvirus 1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')H,F19Human alphaherpesvirus 1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.510α = 90.00
b = 100.730β = 90.00
c = 201.890γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited StatesAI107803

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references