2BOP | pdb_00002bop

CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET

• PDB DOI: https://doi.org/10.2210/pdb2BOP/pdb
• NAKB: 2BOP

• Classification: TRANSCRIPTION/DNA
• Organism(s): Deltapapillomavirus 4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1994-01-13 Released: 1994-01-31 
• Deposition Author(s): Hegde, R.S., Grossman, S.R., Laimins, L.A., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target.

Hegde, R.S., Grossman, S.R., Laimins, L.A., Sigler, P.B.

(1992) Nature 359: 505-512

• PubMed: 1328886 
• DOI: https://doi.org/10.1038/359505a0
• Primary Citation Related Structures: 
  2BOP


• PubMed Abstract: 
  

  The dominant transcriptional regulator of the papillomaviruses, E2, binds to its specific DNA target through a previously unobserved dimeric antiparallel beta-barrel. The DNA is severely but smoothly bent over the barrel by the interaction of successive major grooves with a pair of symmetrically disposed alpha-helices. The specific interface is an 'interwoven' network of interactions where the identifying base pairs of the target contact more than one amino-acid side chain and the discriminating amino acids interact with more than one base pair.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06510.

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: 15.16 kDa 
• Atom Count: 1,144 
• Modeled Residue Count: 102 
• Deposited Residue Count: 102 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (E2)	B [auth A]	85	Deltapapillomavirus 4	Mutation(s): 0
UniProt
Find proteins for P03122 (Bovine papillomavirus type 1) Explore P03122  Go to UniProtKB:  P03122

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*TP*CP*G )-3')	A [auth B]	17	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YB	C [auth B], D [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.201 (Depositor) 

Space Group: R 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.6	α = 61.8
b = 64.6	β = 61.8
c = 64.6	γ = 61.8

Software Package:

Software Name	Purpose
NUCLSQ	refinement
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Hegde, R.S., Grossman, S.R., Laimins, L.A., Sigler, P.B.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-20
  Changes: Advisory, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations