› 5mhk

X-ray diffraction
2.28Å resolution

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

Released:
DOI: 10.2210/pdb5mhk/pdb
PDB entry 5mhk coloured by chain, front view.
PDB entry 5mhk coloured by chain, side view.
PDB entry 5mhk coloured by chain, top view.
Source organism: Human alphaherpesvirus 1
Primary publication:
The herpes viral transcription factor ICP4 forms a novel DNA recognition complex.
Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP
OpenAccess logo Nucleic Acids Res 45 8064-8078 (2017)
PMID: 28505309

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-119025 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Major viral transcription factor ICP4 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 231 amino acids
Theoretical weight: 24.4 KDa
Source organism: Human alphaherpesvirus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P08392 (Residues: 258-487; Coverage: 18%)
Gene names: ICP4, IE175, RS1
Sequence domains: Herpesvirus ICP4-like protein N-terminal region
Major viral transcription factor ICP4 Chain: J
Molecule details ›
Chain: J
Length: 4 amino acids
Theoretical weight: 394 Da
Source organism: Human alphaherpesvirus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P08392 (Residues: 283-286; Coverage: 0%)
Gene names: ICP4, IE175, RS1
DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 19 nucleotides
Theoretical weight: 5.88 KDa
DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 19 nucleotides
Theoretical weight: 5.78 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand SO4 7 x SO4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 61.51Å b: 100.73Å c: 201.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.212 0.243
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Deep structural insights into RNA-binding disordered protein regions.
Zeke et al. (2022)
2 more

2 mentions without citation

Structural basis of specific DNA binding by the transcription factor ZBTB24.
Ren et al. (2019)
1 more