2BZF | pdb_00002bzf

Structural basis for DNA bridging by barrier-to-autointegration factor (BAF)

• PDB DOI: https://doi.org/10.2210/pdb2BZF/pdb
• NAKB: 2BZF

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-08-16 Released: 2005-09-15 
• Deposition Author(s): Bradley, C.M., Ronning, D.R., Ghirlando, R., Craigie, R., Dyda, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.268 (Depositor) 
• R-Value Work: 
  0.244 (Depositor) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for DNA Bridging by Barrier-to-Autointegration Factor.

Bradley, C.M., Ronning, D.R., Ghirlando, R., Craigie, R., Dyda, F.

(2005) Nat Struct Mol Biol 12: 935

• PubMed: 16155580 
• DOI: https://doi.org/10.1038/nsmb989
• Primary Citation Related Structures: 
  2BZF


• PubMed Abstract: 
  

  The ability of barrier-to-autointegration factor (BAF) to bind and bridge DNA in a sequence-independent manner is crucial for its role in retroviral integration and a variety of cellular processes. To better understand this behavior, we solved the crystal structure of BAF bound to DNA. The structure reveals that BAF bridges DNA using two pairs of helix-hairpin-helix motifs located on opposite surfaces of the BAF dimer without changing its conformation.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, US National Institutes of Health (NIH), 5 Center Drive, Bethesda, Maryland 20892, USA.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 14.31 kDa 
• Atom Count: 983 
• Modeled Residue Count: 102 
• Deposited Residue Count: 103 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BARRIER-TO-AUTOINTEGRATION FACTOR	A	89	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75531 (Homo sapiens) Explore O75531  Go to UniProtKB:  O75531
PHAROS:  O75531 GTEx:  ENSG00000175334

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*GP*GP*AP*GP*GP)-3'	B	7	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*TP*CP*CP*AP*CP)-3'	C	7	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.268 (Depositor) 
• R-Value Work:  0.244 (Depositor) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.83	α = 90
b = 45.83	β = 90
c = 241.92	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-15 
Deposition Author(s): Bradley, C.M., Ronning, D.R., Ghirlando, R., Craigie, R., Dyda, F.

Revision History  

• Version 1.0: 2005-09-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Refinement description