Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 65.35 kDa 
• Atom Count: 4563 
• Modelled Residue Count: 558 
• Deposited Residue Count: 568 
• Unique protein chains: 1

2R83

Crystal structure analysis of human synaptotagmin 1 C2A-C2B

• PDB DOI: 10.2210/pdb2R83/pdb

• Classification: ENDOCYTOSIS, EXOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2007-09-10 Released: 2008-02-12 
• Deposition Author(s): Sutton, R.B., Fuson, K.L., Montes, M., Robert, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.253 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Structure of human synaptotagmin 1 C2AB in the absence of Ca2+ reveals a novel domain association.

Fuson, K.L., Montes, M., Robert, J.J., Sutton, R.B.

(2007) Biochemistry 46: 13041-13048

• PubMed: 17956130 
• DOI: 10.1021/bi701651k
• Primary Citation of Related Structures:  
  2R83


• PubMed Abstract: 
  

Release of neurotransmitter from synaptic vesicles requires the Ca2+/phospholipid-binding protein synaptotagmin 1. There is considerable evidence that cooperation between the tandem C2 domains of synaptotagmin is a requirement of regulated exocytosis; however, high-resolution structural evidence for this interaction has been lacking. The 2.7 A crystal structure of the cytosolic domains of human synaptotagmin 1 in the absence of Ca2+ reveals a novel closed conformation of the protein. The shared interface between C2A and C2B is stabilized by a network of interactions between residues on the C-terminal alpha-helix of the C2B domain and residues on loops 1-3 of the Ca2+-binding region of C2A. These interactions alter the overall shape of the Ca2+-binding pocket of C2A, but not that of C2B. Thus, synaptotagmin 1 C2A-C2B may utilize a novel regulatory mechanism whereby one C2 domain could regulate the other until an appropriate triggering event decouples them.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-1	A, B	284	Homo sapiens	Mutation(s): 0  Gene Names: SYT1, SVP65, SYT Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens) Explore P21579  Go to UniProtKB:  P21579
PHAROS:  P21579

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.253 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.372	α = 90
b = 86.31	β = 90
c = 147.186	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
ADSC	data collection
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-09-10 
• Released Date: 2008-02-12 
Deposition Author(s): Sutton, R.B., Fuson, K.L., Montes, M., Robert, J.J.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary