1F08 | pdb_00001f08

CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF THE REPLICATION INITIATION PROTEIN E1 FROM PAPILLOMAVIRUS

• PDB DOI: https://doi.org/10.2210/pdb1F08/pdb

• Classification: REPLICATION
• Organism(s): Bovine papillomavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-05-15 Released: 2001-05-16 
• Deposition Author(s): Enemark, E.J., Chen, G., Vaughn, D.E., Stenlund, A., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.271 (Depositor) 
• R-Value Work: 
  0.241 (Depositor) 

Literature

Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus.

Enemark, E.J., Chen, G., Vaughn, D.E., Stenlund, A., Joshua-Tor, L.

(2000) Mol Cell 6: 149-158

• PubMed: 10949036 
• Primary Citation Related Structures: 
  1F08


• PubMed Abstract: 
  

  Papillomaviral infection causes both benign and malignant lesions and is a necessary cause of cervical carcinoma. Replication of this virus requires the replication initiation proteins E1 and E2, which bind cooperatively at the origin of replication (ori) as an (E1)2-(E2)2-DNA complex. This is a precursor to larger E1 complexes that distort and unwind the ori. We present the crystal structure of the E1 DNA binding domain refined to 1.9 A resolution. Residues critical for DNA binding are located on an extended loop and an alpha helix. We identify the E1 dimerization surface by selective mutations at an E1/E1 interface observed in the crystal and propose a model for the (E1)2-DNA complex. These and other observations suggest how the E1 DNA binding domain orchestrates assembly of the hexameric helicase on the ori.

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Organizational Affiliation: 
• W.M. Keck Structural Biology Center, Cold Spring Harbor, New York 11724, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.87 kDa 
• Atom Count: 2,463 
• Modeled Residue Count: 293 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REPLICATION PROTEIN E1	A, B	148	Bovine papillomavirus	Mutation(s): 0  EC: 5.6.2.4
UniProt
Find proteins for P03116 (Bovine papillomavirus type 1) Explore P03116  Go to UniProtKB:  P03116

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.271 (Depositor) 
• R-Value Work:  0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.17	α = 90
b = 84.897	β = 90
c = 124.276	γ = 90

Software Package:

Software Name	Purpose
SnB	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-16 
Deposition Author(s): Enemark, E.J., Chen, G., Vaughn, D.E., Stenlund, A., Joshua-Tor, L.

Revision History  

• Version 1.0: 2001-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2024-02-07
  Changes: Advisory, Data collection, Database references, Derived calculations