1Z1B

Crystal structure of a lambda integrase dimer bound to a COC' core site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A structural basis for allosteric control of DNA recombination by lambda integrase.

Biswas, T.Aihara, H.Radman-Livaja, M.Filman, D.Landy, A.Ellenberger, T.

(2005) Nature 435: 1059-1066

  • DOI: https://doi.org/10.1038/nature03657
  • Primary Citation of Related Structures:  
    1Z19, 1Z1B, 1Z1G

  • PubMed Abstract: 

    Site-specific DNA recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage lambda to integrate or excise its genome into and out of the host chromosome. lambda recombination is carried out by the bacteriophage-encoded integrase protein (lambda-int) together with accessory DNA sites and associated bending proteins that allow regulation in response to cell physiology. Here we report the crystal structures of lambda-int in higher-order complexes with substrates and regulatory DNAs representing different intermediates along the reaction pathway. The structures show how the simultaneous binding of two separate domains of lambda-int to DNA facilitates synapsis and can specify the order of DNA strand cleavage and exchange. An intertwined layer of amino-terminal domains bound to accessory (arm) DNAs shapes the recombination complex in a way that suggests how arm binding shifts the reaction equilibrium in favour of recombinant products.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.


Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
IntegraseF [auth A],
G [auth B]
356Lambdavirus lambdaMutation(s): 2 
Gene Names: INT
UniProt
Find proteins for P03700 (Escherichia phage lambda)
Explore P03700 
Go to UniProtKB:  P03700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03700
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'A [auth C]14N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T)-3'B [auth D]18N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
29-MER DNAC [auth E]29N/A
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Entity ID: 4
MoleculeChains LengthOrganismImage
26-MER DNAD [auth F]26N/A
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Entity ID: 5
MoleculeChains LengthOrganismImage
26-MER DNAE [auth G]26N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
F [auth A],
G [auth B]
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.599α = 90
b = 211.278β = 90
c = 191.704γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
SHARPphasing
REFMACrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-28
    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: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2022-04-13
    Changes: Structure summary