5MHJ | pdb_00005mhj

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

• PDB DOI: https://doi.org/10.2210/pdb5MHJ/pdb
• NAKB: 5MHJ

• Classification: TRANSCRIPTION
• Organism(s): Human alphaherpesvirus 1 strain 17, Human alphaherpesvirus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-24 Released: 2017-05-24 
• Deposition Author(s): Tunnicliffe, R.B., Lockhart-Cairns, M.P., Levy, C., Mould, P., Jowitt, T.A., Sito, H., Baldock, C., Sandri-Goldin, R.M., Golovanov, A.P.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: other

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

• PubMed: 28505309 
• DOI: https://doi.org/10.1093/nar/gkx419
• Primary Citation 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.

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Organizational Affiliation: 
• Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, UK.
Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK.
Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0QX, UK.
Biomolecular Analysis Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK.
Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.11 kDa 
• Atom Count: 3,476 
• Modeled Residue Count: 399 
• Deposited Residue Count: 426 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major viral transcription factor ICP4	A, B	201	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: ICP4, IE175, RS1
UniProt
Find proteins for P08392 (Human herpesvirus 1 (strain 17)) Explore P08392  Go to UniProtKB:  P08392

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')	C [auth E]	12	Human alphaherpesvirus 1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)-3')	D [auth F]	12	Human alphaherpesvirus 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	E [auth A], G [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.254	α = 90
b = 39.084	β = 90
c = 90.443	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Tunnicliffe, R.B., Lockhart-Cairns, M.P., Levy, C., Mould, P., Jowitt, T.A., Sito, H., Baldock, C., Sandri-Goldin, R.M., Golovanov, A.P.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	AI107803

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
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Refinement description