1TJF | pdb_00001tjf

The crystal structure of the N-terminal domain of CAP indicates variable oligomerisation

• PDB DOI: https://doi.org/10.2210/pdb1TJF/pdb

• Classification: MEMBRANE PROTEIN, PROTEIN BINDING
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-04 Released: 2005-02-01 
• Deposition Author(s): Mohd Yusof, A., Hu, N.J., Wlodawer, A., Hofmann, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural evidence for variable oligomerization of the N-terminal domain of cyclase-associated protein (CAP).

Mohd Yusof, A., Hu, N.J., Wlodawer, A., Hofmann, A.

(2005) Proteins 58: 255-262

• PubMed: 15558566 
• DOI: https://doi.org/10.1002/prot.20314
• Primary Citation Related Structures: 
  1TJF


• PubMed Abstract: 
  

  Cyclase-associated protein (CAP) is a highly conserved and widely distributed protein that links the nutritional response signaling to cytoskeleton remodeling. In yeast, CAP is a component of the adenylyl cyclase complex and helps to activate the Ras-mediated catalytic cycle of the cyclase. While the N-terminal domain of CAP (N-CAP) provides a binding site for adenylyl cyclase, the C-terminal domain (C-CAP) possesses actin binding activity. Our attempts to crystallize full-length recombinant CAP from Dictyostelium discoideum resulted in growth of orthorhombic crystals containing only the N-terminal domain (residues 42-227) due to auto-proteolytic cleavage. The structure was solved by molecular replacement with data at 2.2 A resolution. The present crystal structure allows the characterization of a head-to-tail N-CAP dimer in the asymmetric unit and a crystallographic side-to-side dimer. Comparison with previously published structures of N-CAP reveals variable modes of dimerization of this domain, but the presence of a common interface for the side-to-side dimer.

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Organizational Affiliation: 
• Institute of Structural & Molecular Biology, School of Biological Sciences, The University of Edinburgh, Scotland, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.5 kDa 
• Atom Count: 3,169 
• Modeled Residue Count: 371 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl cyclase-associated protein	A, B	186	Dictyostelium discoideum	Mutation(s): 0  Gene Names: CAP
UniProt
Find proteins for P54654 (Dictyostelium discoideum) Explore P54654  Go to UniProtKB:  P54654

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.24	α = 90
b = 75.06	β = 90
c = 162.874	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Mohd Yusof, A., Hu, N.J., Wlodawer, A., Hofmann, A.

Revision History  

• Version 1.0: 2005-02-01
  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: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description