Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 246.27 kDa 
• Atom Count: 15798 
• Residue Count: 2060 
• Unique protein chains: 1

1URJ

Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1

• DOI: 10.2210/pdb1URJ/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Human alphaherpesvirus 1
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2003-10-30 Released: 2004-11-11 
• Deposition Author(s): Panjikar, S., Mapelli, M., Tucker, P.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.286 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 

Literature

The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding.

Mapelli, M., Panjikar, S., Tucker, P.A.

(2005) J Biol Chem 280: 2990-2997

• PubMed: 15507432 
• DOI: 10.1074/jbc.M406780200
• Primary Citation of Related Structures:  
  1URJ


• PubMed Abstract: 
  

All organisms including animal viruses use specific proteins to bind single-stranded DNA rapidly in a non-sequence-specific, flexible, and cooperative manner during the DNA replication process. The crystal structure of a 60-residue C-terminal deletion construct of ICP8, the major single-stranded DNA-binding protein from herpes simplex virus-1, was determined at 3.0 A resolution. The structure reveals a novel fold, consisting of a large N-terminal domain (residues 9-1038) and a small C-terminal domain (residues 1049-1129). On the basis of the structure and the nearest neighbor interactions in the crystal, we have presented a model describing the site of single-stranded DNA binding and explaining the basis for cooperative binding. This model agrees with the beaded morphology observed in electron micrographs.

---

Organizational Affiliation: 

European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR DNA-BINDING PROTEIN	A, B	1136	Human alphaherpesvirus 1	Mutation(s): 2
Find proteins for P04296 (Human herpesvirus 1 (strain 17)) Explore P04296  Go to UniProtKB:  P04296

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	A, B	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.286 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.91	α = 90
b = 145.37	β = 90
c = 162.03	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
SHELXD	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-30 
• Released Date: 2004-11-11 
Deposition Author(s): Panjikar, S., Mapelli, M., Tucker, P.A.

Revision History 

• Version 1.0: 2004-11-11
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-10-17
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.4: 2019-07-10
  Changes: Data collection, Structure summary
• Version 1.5: 2019-07-24
  Changes: Data collection