1RSY | pdb_00001rsy

STRUCTURE OF THE FIRST C2-DOMAIN OF SYNAPTOTAGMIN I: A NOVEL CA2+(SLASH)PHOSPHOLIPID BINDING FOLD

• PDB DOI: https://doi.org/10.2210/pdb1RSY/pdb

• Classification: CALCIUM/PHOSPHOLIPID BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1995-02-01 Released: 1995-05-08 
• Deposition Author(s): Sutton, R.B., Sprang, S.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.249 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4WEE

Literature

Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold.

Sutton, R.B., Davletov, B.A., Berghuis, A.M., Sudhof, T.C., Sprang, S.R.

(1995) Cell 80: 929-938

• PubMed: 7697723 
• DOI: https://doi.org/10.1016/0092-8674(95)90296-1
• Primary Citation of Related Structures:  
  1RSY


• PubMed Abstract: 
  

  C2 domains are regulatory sequence motifs that occur widely in nature. Synaptotagmin I, a synaptic vesicle protein involved in the Ca2+ regulation of exocytosis, contains two C2 domains, the first of which acts as a Ca2+ sensor. We now describe the three-dimensional structure of this C2 domain at 1.9 A resolution in both the Ca(2+)-bound and Ca(2+)-free forms. The C2 polypeptide forms an eight-stranded beta sandwich constructed around a conserved four-stranded motif designated as a C2 key. Ca2+ binds in a cup-shaped depression between two polypeptide loops located at the N- and C-termini of the C2-key motif.

---

Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.19 kDa 
• Atom Count: 1,151 
• Modeled Residue Count: 135 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPTOTAGMIN I	A	152	Rattus norvegicus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P21707 (Rattus norvegicus) Explore P21707  Go to UniProtKB:  P21707

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.249 (Depositor) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.3	α = 90
b = 38.9	β = 96.9
c = 44.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-05-08 
Deposition Author(s): Sutton, R.B., Sprang, S.R.

Revision History  

• Version 1.0: 1995-05-08
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other