1RIO

Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb1RIO/pdb
• NAKB: 1RIO

• Classification: transcription/DNA
• Organism(s): Thermus aquaticus, Lambdavirus lambda
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-11-17 Released: 2004-01-27 
• Deposition Author(s): Jain, D., Nickels, B.E., Sun, L., Hochschild, A., Darst, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Structure of a ternary transcription activation complex.

Jain, D., Nickels, B.E., Sun, L., Hochschild, A., Darst, S.A.

(2004) Mol Cell 13: 45-53

• PubMed: 14731393 
• DOI: https://doi.org/10.1016/s1097-2765(03)00483-0
• Primary Citation of Related Structures:  
  1RIO


• PubMed Abstract: 
  

  The cI protein of bacteriophage lambda (lambdacI) activates transcription by binding a DNA operator just upstream of the promoter and interacting with the RNA polymerase sigma subunit domain 4 (sigma(4)). We determined the crystal structure of the lambdacI/sigma(4)/DNA ternary complex at 2.3 A resolution. There are no conformational changes in either protein, which interact through an extremely small interface involving at most 6 amino acid residues. The interactions of the two proteins stabilize the binding of each protein to the DNA. The results provide insight into how activators can operate through a simple cooperative binding mechanism but affect different steps of the transcription initiation process.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.77 kDa 
• Atom Count: 3,286 
• Modelled Residue Count: 308 
• Deposited Residue Count: 323 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
sigma factor SigA	C [auth H]	73	Thermus aquaticus	Mutation(s): 0
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus) Explore Q9EZJ8  Go to UniProtKB:  Q9EZJ8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Repressor protein CI	D [auth A], E [auth B]	98	Lambdavirus lambda	Mutation(s): 3  Gene Names: CI
UniProt
Find proteins for P03034 (Escherichia phage lambda) Explore P03034  Go to UniProtKB:  P03034

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	D [auth A], E [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.256	α = 90
b = 71.269	β = 91.34
c = 77.199	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Jain, D., Nickels, B.E., Sun, L., Hochschild, A., Darst, S.A.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary