3BDN

Crystal Structure of the Lambda Repressor

• PDB DOI:  https://doi.org/10.2210/pdb3BDN/pdb
• NAKB: 3BDN

• Classification: TRANSCRIPTION/DNA
• Organism(s): Lambdavirus lambda
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-11-15 Released: 2008-04-15 
• Deposition Author(s): Stayrook, S.E., Jaru-Ampornpan, P., Hochschild, A., Lewis, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.91 Å
• R-Value Free: 0.374 
• R-Value Work: 0.292 
• R-Value Observed: 0.296 

Literature

Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding

Stayrook, S.E., Jaru-Ampornpan, P., Ni, J., Hochschild, A., Lewis, M.

(2008) Nature 452: 1022-1025

• PubMed: 18432246 
• DOI: https://doi.org/10.1038/nature06831
• Primary Citation of Related Structures:  
  3BDN


• PubMed Abstract: 
  

Bacteriophage lambda has for many years been a model system for understanding mechanisms of gene regulation. A 'genetic switch' enables the phage to transition from lysogenic growth to lytic development when triggered by specific environmental conditions. The key component of the switch is the cI repressor, which binds to two sets of three operator sites on the lambda chromosome that are separated by about 2,400 base pairs (bp). A hallmark of the lambda system is the pairwise cooperativity of repressor binding. In the absence of detailed structural information, it has been difficult to understand fully how repressor molecules establish the cooperativity complex. Here we present the X-ray crystal structure of the intact lambda cI repressor dimer bound to a DNA operator site. The structure of the repressor, determined by multiple isomorphous replacement methods, reveals an unusual overall architecture that allows it to adopt a conformation that appears to facilitate pairwise cooperative binding to adjacent operator sites.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, Pennsylvania 19102-6059, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.36 kDa 
• Atom Count: 4,405 
• Modelled Residue Count: 506 
• Deposited Residue Count: 512 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lambda Repressor	C [auth A], D [auth B]	236	Lambdavirus lambda	Mutation(s): 1  Gene Names: cI, lambdap88
UniProt
Find proteins for P03034 (Escherichia phage lambda) Explore P03034  Go to UniProtKB:  P03034

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DAP*DTP*DAP*DT)-3')	A [auth C]	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DTP*DAP*DTP*DAP*DTP*DCP*DAP*DCP*DCP*DGP*DCP*DCP*DAP*DGP*DTP*DGP*DGP*DTP*DAP*DT)-3')	B [auth D]	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.91 Å
• R-Value Free: 0.374 
• R-Value Work: 0.292 
• R-Value Observed: 0.296 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.431	α = 90
b = 161.099	β = 90
c = 135.256	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MLPHARE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Stayrook, S.E., Jaru-Ampornpan, P., Hochschild, A., Lewis, M.

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description