1LB2 | pdb_00001lb2

Structure of the E. coli alpha C-terminal domain of RNA polymerase in complex with CAP and DNA

• PDB DOI: https://doi.org/10.2210/pdb1LB2/pdb
• NAKB: 1LB2

• Classification: GENE REGULATION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-04-01 Released: 2002-09-06 
• Deposition Author(s): Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., Ebright, R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.216 (DCC) 

Starting Model: experimental

Literature

Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.

Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., Ebright, R.H.

(2002) Science 297: 1562-1566

• PubMed: 12202833 
• DOI: https://doi.org/10.1126/science.1076376
• Primary Citation Related Structures: 
  1LB2


• PubMed Abstract: 
  

  The Escherichia coli catabolite activator protein (CAP) activates transcription at P(lac), P(gal), and other promoters through interactions with the RNA polymerase alpha subunit carboxyl-terminal domain (alphaCTD). We determined the crystal structure of the CAP-alphaCTD-DNA complex at a resolution of 3.1 angstroms. CAP makes direct protein-protein interactions with alphaCTD, and alphaCTD makes direct protein-DNA interactions with the DNA segment adjacent to the DNA site for CAP. There are no large-scale conformational changes in CAP and alphaCTD, and the interface between CAP and alphaCTD is small. These findings are consistent with the proposal that activation involves a simple "recruitment" mechanism.

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Organizational Affiliation: 
• Waksman Institute and Department of Chemistry, Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.1 kDa 
• Atom Count: 3,613 
• Modeled Residue Count: 383 
• Deposited Residue Count: 421 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CATABOLITE GENE ACTIVATOR PROTEIN	C [auth A]	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8  Go to UniProtKB:  P0ACJ8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase alpha chain	D [auth B], E	84	Escherichia coli	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4  Go to UniProtKB:  P0A7Z4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'	A [auth K]	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3'	B [auth J]	24	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	F [auth A]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.216 (DCC) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.97	α = 90
b = 175.97	β = 90
c = 158.02	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-06 
Deposition Author(s): Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., Ebright, R.H.

Revision History  

• Version 1.0: 2002-09-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description