6A68 | pdb_00006a68

the crystal structure of rat calcium-dependent activator protein for secretion (CAPS) DAMH domain

• PDB DOI: https://doi.org/10.2210/pdb6A68/pdb

• Classification: EXOCYTOSIS
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-06-26 Released: 2019-03-13 
• Deposition Author(s): Zhou, H., Wei, Z.Q., Yao, D.Q., Zhang, R.G., Ma, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Structural and Functional Analysis of the CAPS SNARE-Binding Domain Required for SNARE Complex Formation and Exocytosis.

Zhou, H., Wei, Z., Wang, S., Yao, D., Zhang, R., Ma, C.

(2019) Cell Rep 26: 3347-3359.e6

• PubMed: 30893606 
• DOI: https://doi.org/10.1016/j.celrep.2019.02.064
• Primary Citation of Related Structures:  
  6A68


• PubMed Abstract: 
  

  Exocytosis of synaptic vesicles and dense-core vesicles requires both the Munc13 and CAPS (Ca ²⁺ -dependent activator proteins for secretion) proteins. CAPS contains a soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-binding region (called the DAMH domain), which has been found to be essential for SNARE-mediated exocytosis. Here we report a crystal structure of the CAPS-1 DAMH domain at 2.9-Å resolution and reveal a dual role of CAPS-1 in SNARE complex formation. CAPS-1 plays an inhibitory role dependent on binding of the DAMH domain to the MUN domain of Munc13-1, which hinders the ability of Munc13 to catalyze opening of syntaxin-1, inhibiting SNARE complex formation, and a chaperone role dependent on interaction of the DAMH domain with the syntaxin-1/SNAP-25 complex, which stabilizes the open conformation of Syx1, facilitating SNARE complex formation. Our results suggest that CAPS-1 facilitates SNARE complex formation via the DAMH domain in a manner dependent on sequential and cooperative interaction with Munc13-1 and SNARE proteins.

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Organizational Affiliation: 
• Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China.
National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, 201203 Shanghai, China.
National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, 201203 Shanghai, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China.
Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.6 kDa 
• Atom Count: 1,294 
• Modeled Residue Count: 162 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent secretion activator 1	A	184	Rattus norvegicus	Mutation(s): 0  Gene Names: Cadps, Caps, Caps1
UniProt
Find proteins for Q62717 (Rattus norvegicus) Explore Q62717  Go to UniProtKB:  Q62717

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.305	α = 90
b = 149.305	β = 90
c = 81.414	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Zhou, H., Wei, Z.Q., Yao, D.Q., Zhang, R.G., Ma, C.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary