6BUS | pdb_00006bus

Extended E2 DNA-binding domain of the Bovine Papillomavirus-1

• PDB DOI: https://doi.org/10.2210/pdb6BUS/pdb

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


• Deposited: 2017-12-11 Released: 2018-01-10 
• Deposition Author(s): Leroy, L.M.D., Barbosa, J.A.R.G., Polikarpov, I., Pinheiro, C.B.
• Funding Organization(s): Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.261 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

The structure of the extended E2 DNA-binding domain of the bovine papillomavirus-1.

Leroy, L., Barbosa, J.A.R.G., de Prat-Gay, G., Polikarpov, I., Pinheiro, C.B.

(2020) Proteins 88: 106-112

• PubMed: 31299114 
• DOI: https://doi.org/10.1002/prot.25773
• Primary Citation Related Structures: 
  6BUS


• PubMed Abstract: 
  

  Bovine papillomavirus proteins were extensively studied as a prototype for the human papillomavirus. Here, the crystal structure of the extended E2 DNA-binding domain of the dominant transcription regulator from the bovine papillomavirus strain 1 is described in the space group P3 ₁ 21. We found two protein functional dimers packed in the asymmetric unit. This new protein arrangement inside the crystal led to the reduction of the mobility of a previously unobserved loop directly involved in the protein-DNA interaction, which was then modeled for the first time.

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Organizational Affiliation: 
• Laboratório de Cristalografia, Physics Department, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Laboratory of Molecular Biophysics, Department of Celular Biology, Universidade de Brasília, Brasília, Brazil.
Fundación Instituto Leloir, CABA, Buenos Aires, Argentina.
Instituto de Física de São Carlos, Universidade de São Paulo, São Calos, Brazil.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 46.31 kDa 
• Atom Count: 3,118 
• Modeled Residue Count: 371 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein E2	A [auth 1], B [auth 2], C [auth 3], D [auth 4]	103	Deltapapillomavirus 4	Mutation(s): 0  Gene Names: E2
UniProt
Find proteins for P03122 (Bovine papillomavirus type 1) Explore P03122  Go to UniProtKB:  P03122

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.261 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.203	α = 90
b = 55.203	β = 90
c = 203.091	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Leroy, L.M.D., Barbosa, J.A.R.G., Polikarpov, I., Pinheiro, C.B.

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Funding Organization	Location	Grant Number
Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior	Brazil	--

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description