1KSY | pdb_00001ksy

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex

• PDB DOI: https://doi.org/10.2210/pdb1KSY/pdb
• NAKB: 1KSY

• Classification: REPLICATION/DNA
• Organism(s): Bovine papillomavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-01-14 Released: 2002-03-15 
• Deposition Author(s): Enemark, E.J., Stenlund, A., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.316 (Depositor) 
• R-Value Work: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex.

Enemark, E.J., Stenlund, A., Joshua-Tor, L.

(2002) EMBO J 21: 1487-1496

• PubMed: 11889054 
• DOI: https://doi.org/10.1093/emboj/21.6.1487
• Primary Citation Related Structures: 
  1KSX, 1KSY


• PubMed Abstract: 
  

  Initiation of DNA replication of the papillomavirus genome is a multi-step process involving the sequential loading of viral E1 protein subunits onto the origin of replication. Here we have captured structural snapshots of two sequential steps in the assembly process. Initially, an E1 dimer binds to adjacent major grooves on one face of the double helix; a second dimer then binds to another face of the helix. Each E1 monomer has two DNA-binding modules: a DNA-binding loop, which binds to one DNA strand and a DNA-binding helix, which binds to the opposite strand. The nature of DNA binding suggests a mechanism for the transition between double- and single-stranded DNA binding that is implicit in the progression to a functional helicase.

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Organizational Affiliation: 
• W.M.Keck Structural Biology Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.01 kDa 
• Atom Count: 4,795 
• Modeled Residue Count: 501 
• Deposited Residue Count: 525 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REPLICATION PROTEIN E1	D [auth A], E [auth B], F [auth C]	154	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
E1 Recognition Sequence, Strand 1	A [auth D], B [auth E]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
E1 Recognition Sequence, Strand 2	C [auth F]	21	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.316 (Depositor) 
• R-Value Work:  0.277 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.111	α = 90
b = 110.6	β = 116.85
c = 75.084	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-15 
Deposition Author(s): Enemark, E.J., Stenlund, A., Joshua-Tor, L.

Revision History  

• Version 1.0: 2002-03-15
  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: 2023-08-16
  Changes: Data collection, Database references, Refinement description