1CGP | pdb_00001cgp

CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1CGP/pdb
• NAKB: 1CGP

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Escherichia coli
• Mutation(s): No 


• Deposited: 1991-08-12 Released: 1994-01-31 
• Deposition Author(s): Schultz, S.C., Shields, G.C., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 
  0.235 (Depositor) 

Literature

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.

Schultz, S.C., Shields, G.C., Steitz, T.A.

(1991) Science 253: 1001-1007

• PubMed: 1653449 
• DOI: https://doi.org/10.1126/science.1653449
• Primary Citation of Related Structures:  
  1CGP


• PubMed Abstract: 
  

  The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This bend results almost entirely from two 40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor--DNA complex provides insights into possible mechanisms of transcription activation.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.8 kDa 
• Atom Count: 4,418 
• Modeled Residue Count: 456 
• Deposited Residue Count: 472 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP))	E [auth A], F [auth B]	205	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8  Go to UniProtKB:  P0ACJ8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')	A [auth C], C [auth E]	18	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G)-3')	B [auth D], D [auth F]	13	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work:  0.235 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138	α = 90
b = 152.6	β = 90
c = 76	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Schultz, S.C., Shields, G.C., Steitz, T.A.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-15
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations