1IHW | pdb_00001ihw

SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HIV-1 INTEGRASE, NMR, 40 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1IHW/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-05-12 Released: 1996-07-11 
• Deposition Author(s): Clore, G.M., Lodi, P.J., Ernst, J.A., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 40 

Literature

Solution structure of the DNA binding domain of HIV-1 integrase.

Lodi, P.J., Ernst, J.A., Kuszewski, J., Hickman, A.B., Engelman, A., Craigie, R., Clore, G.M., Gronenborn, A.M.

(1995) Biochemistry 34: 9826-9833

• PubMed: 7632683 
• DOI: https://doi.org/10.1021/bi00031a002
• Primary Citation Related Structures: 
  1IHV, 1IHW


• PubMed Abstract: 
  

  The solution structure of the DNA binding domain of HIV-1 integrase (residues 220-270) has been determined by multidimensional NMR spectroscopy. The protein is a dimer in solution, and each subunit is composed of a five-stranded beta-barrel with a topology very similar to that of the SH3 domain. The dimer is formed by a stacked beta-interface comprising strands 2, 3, and 4, with the two triple-stranded antiparallel beta-sheets, one from each subunit, oriented antiparallel to each other. One surface of the dimer, bounded by the loop between strands beta 1 and beta 2, forms a saddle-shaped groove with dimensions of approximately 24 x 23 x 12 A in cross section. Lys264, which has been shown from mutational data to be involved in DNA binding, protrudes from this surface, implicating the saddle-shaped groove as the potential DNA binding site.

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Organizational Affiliation: 
• Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.

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: 12.28 kDa 
• Atom Count: 866 
• Modeled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 INTEGRASE	A, B	52	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04586 (Human immunodeficiency virus type 1 group M subtype D (isolate Z6)) Explore P04586  Go to UniProtKB:  P04586

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 40 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-07-11 
Deposition Author(s): Clore, G.M., Lodi, P.J., Ernst, J.A., Gronenborn, A.M.

Revision History  

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.4: 2024-05-22
  Changes: Data collection