Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.50 kDa 
• Atom Count: 1584 
• Modelled Residue Count: 200 
• Deposited Residue Count: 200 
• Unique protein chains: 1

1DBD

E2 DNA-BINDING DOMAIN FROM PAPILLOMAVIRUS BPV-1

• PDB DOI: 10.2210/pdb1DBD/pdb
• BMRB: 4087

• Classification: GENE REGULATION
• Organism(s): Deltapapillomavirus 4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-05-21 Released: 2000-01-01 
• Deposition Author(s): Veeraraghavan, S., Mello, C.C., Androphy, E.J., Baleja, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 1 
• Selection Criteria: MINIMIZED AVERAGE 

Literature

Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus.

Veeraraghavan, S., Mello, C.C., Androphy, E.J., Baleja, J.D.

(1999) Biochemistry 38: 16115-16124

• PubMed: 10587434 
• DOI: 10.1021/bi991633x
• Primary Citation of Related Structures:  
  1DBD


• PubMed Abstract: 
  

Papillomaviral E2 proteins participate in viral DNA replication and transcriptional regulation. We have solved the solution structure of the DNA-binding domain of the E2 protein from bovine papillomavirus (BPV-1). The structure calculation used 2222 distance and 158 dihedral angle restraints for the homodimer (202 residues in total), which were derived from homonuclear and heteronuclear multidimensional nuclear magnetic resonance (NMR) spectroscopic data. The root-mean-square deviation for structured regions of the monomer when superimposed to the average is 0.73 +/- 0.10 A for backbone atoms and 1.42 +/- 0.16 A for heavy atoms. The 101 residue construct used in this study (residues 310-410) is about 4.5 kcal/mol more stable than a minimal domain comprising the C-terminal 85 amino acid residues (residues 326-410). The structure of the core domain contained within BPV-1 E2 is similar to the corresponding regions of other papilloma viral E2 proteins. Here, however, the extra N-terminal 16 residues form a flap that covers a cavity at the dimer interface and play a role in DNA binding. Interactions between residues in the N-terminal extension and the core domain correlate with the greater stability of the longer form of the protein relative to the minimal domain.

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Organizational Affiliation: 

Department of Biochemistry, Tufts University School of Medicine, Boston, MA 02111, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATORY PROTEIN E2	A, B	100	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: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 1 
• Selection Criteria: MINIMIZED AVERAGE 
• OLDERADO: 1DBD Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-21 
• Released Date: 2000-01-01 
Deposition Author(s): Veeraraghavan, S., Mello, C.C., Androphy, E.J., Baleja, J.D.

Revision History  

• Version 1.0: 2000-01-01
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations