1ZS4

Structure of bacteriophage lambda cII protein in complex with DNA

• PDB DOI:  https://doi.org/10.2210/pdb1ZS4/pdb
• NAKB: 1ZS4

• Classification: transcription/DNA
• Organism(s): Lambdavirus lambda
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-23 Released: 2005-08-23 
• Deposition Author(s): Jain, D., Kim, Y., Maxwell, K.L., Beasley, S., Gussin, G.N., Edwards, A.M., Darst, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.228 
• R-Value Work: 0.209 

Literature

Crystal Structure of Bacteriophage lambdacII and Its DNA Complex.

Jain, D., Kim, Y., Maxwell, K.L., Beasley, S., Zhang, R., Gussin, G.N., Edwards, A.M., Darst, S.A.

(2005) Mol Cell 19: 259-269

• PubMed: 16039594 
• DOI: https://doi.org/10.1016/j.molcel.2005.06.006
• Primary Citation of Related Structures:  
  1ZPQ, 1ZS4


• PubMed Abstract: 
  

The tetrameric cII protein from bacteriophage lambda activates transcription from the phage promoters P(RE), P(I), and P(AQ) by binding to two direct repeats that flank the promoter -35 element. Here, we present the X-ray crystal structure of cII alone (2.8 A resolution) and in complex with its DNA operator from P(RE) (1.7 A resolution). The structures provide a basis for modeling of the activation complex with the RNA polymerase holoenzyme, and point to the key role for the RNA polymerase alpha subunit C-terminal domain (alphaCTD) in cII-dependent activation, which forms a bridge of protein/protein interactions between cII and the RNA polymerase sigma subunit. The model makes specific predictions for protein/protein interactions between cII and alphaCTD, and between alphaCTD and sigma, which are supported by previous genetic studies.

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Organizational Affiliation: 

The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.87 kDa 
• Atom Count: 4,012 
• Modelled Residue Count: 370 
• Deposited Residue Count: 386 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein CII	C [auth A], D [auth B], E [auth C], F [auth D]	83	Lambdavirus lambda	Mutation(s): 0  Gene Names: cII, lambdap59
UniProt
Find proteins for P03042 (Escherichia phage lambda) Explore P03042  Go to UniProtKB:  P03042

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA - 27mer	A [auth U]	27	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA - 27mer	B [auth T]	27	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.228 
• R-Value Work: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.771	α = 90
b = 97.132	β = 105.36
c = 59.869	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-23 
Deposition Author(s): Jain, D., Kim, Y., Maxwell, K.L., Beasley, S., Gussin, G.N., Edwards, A.M., Darst, S.A.

Revision History  

• Version 1.0: 2005-08-23
  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: 2011-12-28
  Changes: Advisory