Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19047.94 
• Atom Count: 1336 
• Residue Count: 166 
• Unique protein chains: 1

1DHM

DNA-BINDING DOMAIN OF E2 FROM HUMAN PAPILLOMAVIRUS-31, NMR, MINIMIZED AVERAGE STRUCTURE

• DOI: 10.2210/pdb1DHM/pdb
• BMRB: 4035

• Classification: DNA BINDING PROTEIN
• Organism(s): Human papillomavirus type 31
• Expression System: Escherichia coli


• Deposited: 1995-08-15 Released: 1996-12-07 
• Deposition Author(s): Liang, H., Petros, A.P., Meadows, R.P., Yoon, H.S., Egan, D.A., Walter, K., Holzman, T.F., Robins, T., Fesik, S.W.

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Experimental Data Snapshot

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

Literature

Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions.

Liang, H., Petros, A.M., Meadows, R.P., Yoon, H.S., Egan, D.A., Walter, K., Holzman, T.F., Robins, T., Fesik, S.W.

(1996) Biochemistry 35: 2095-2103

• PubMed: 8652551 
• DOI: 10.1021/bi951932w


• PubMed Abstract: 
  

The three-dimensional structure of the DNA-binding domain of the E2 protein from human papillomavirus-31 was determined by using multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy. A total of 1429 NMR-derived distance and dihedral angle restraints were obtained for each of the 83-residue subunits of this symmetric dimer. The average root mean square deviations of 20 structures calculated using a distance geometry-simulated annealing protocol are 0.59 and 0.90 angstroms for the backbone and all heavy atoms, respectively, for residues 2-83. The structure of the human virus protein free in solution consists of an eight-stranded beta-barrel and two pairs of alpha-helices. Although the overall fold of the protein is similar to the crystal structure of the bovine papillomavirus-1 E2 protein when complexed to DNA, several small but interesting differences were observed between these two structures at the subunit interface. In addition, a beta-hairpin that contacts DNA in the crystal structure of the protein-DNA complex is disordered in the NMR structures, and steady-state 1H-15N heteronuclear NOE measurements indicate that this region is highly mobile in the absence of DNA. The recognition helix also appears to be flexible, as evidenced by fast amide exchange rates. This phenomenon has also been observed for a number of other DNA-binding proteins and may constitute a common theme in protein/DNA recognition.

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Organizational Affiliation: 

Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E2 PROTEIN	A, B	83	Human papillomavirus type 31	Mutation(s): 0  Gene Names: E2
Find proteins for P17383 (Human papillomavirus type 31) Go to UniProtKB:  P17383

Experimental Data & Validation

Experimental Data

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

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-08-15 
• Released Date: 1996-12-07 
• Deposition Author(s): Liang, H., Petros, A.P., Meadows, R.P., Yoon, H.S., Egan, D.A., Walter, K., Holzman, T.F., Robins, T., Fesik, S.W.

Revision History 

• Version 1.0: 1996-12-07
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Source and taxonomy, Version format compliance