Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 201.07 kDa 
• Atom Count: 13236 
• Modelled Residue Count: 1396 
• Deposited Residue Count: 1446 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2A3V

Structural basis for broad DNA-specificity in integron recombination

• PDB DOI: 10.2210/pdb2A3V/pdb
• NDB: PD0690

• Classification: RECOMBINATION
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-27 Released: 2006-05-02 
• Deposition Author(s): MacDonald, D., Demarre, G., Bouvier, M., Mazel, D., Gopaul, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

Literature

Structural basis for broad DNA-specificity in integron recombination.

MacDonald, D., Demarre, G., Bouvier, M., Mazel, D., Gopaul, D.N.

(2006) Nature 440: 1157-1162

• PubMed: 16641988 
• DOI: 10.1038/nature04643
• Primary Citation of Related Structures:  
  2A3V


• PubMed Abstract: 
  

Lateral DNA transfer--the movement of genetic traits between bacteria--has a profound impact on genomic evolution and speciation. The efficiency with which bacteria incorporate genetic information reflects their capacity to adapt to changing environmental conditions. Integron integrases are proteins that mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. The lack of sequence conservation among attC sites has led to the hypothesis that a sequence-independent structural recognition determinant must exist within attC. Here we report the crystal structure of an integron integrase bound to an attC substrate. The structure shows that DNA target site recognition and high-order synaptic assembly are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. These extrahelical bases, one of which is required for recombination in vivo, originate from folding of the bottom strand of attC owing to its imperfect internal dyad symmetry. The mechanism reported here supports a new paradigm for how sequence-degenerate single-stranded genetic material is recognized and exchanged between bacteria.

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Organizational Affiliation: 

Laboratoire de Biochimie et Biophysique des Macromolécules, Département de Biologie Structurale et Chimie, CNRS URA 2171, Institut Pasteur, 75724 Paris Cedex 15, France.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
site-specific recombinase IntI4	E [auth A], F [auth B], G [auth C], H [auth D]	320	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: intI4
UniProt
Find proteins for O68847 (Vibrio cholerae) Explore O68847  Go to UniProtKB:  O68847

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	A [auth E], C [auth G]	40	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	B [auth F], D [auth H]	43	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.9	α = 90
b = 170.2	β = 90
c = 209.4	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SnB	phasing
CNS	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-27 
• Released Date: 2006-05-02 
Deposition Author(s): MacDonald, D., Demarre, G., Bouvier, M., Mazel, D., Gopaul, D.N.

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references