6CXW | pdb_00006cxw

Synaptotagmin 1 C2A beta4 chimera with enhanced PIP2 binding function

• PDB DOI: https://doi.org/10.2210/pdb6CXW/pdb

• Classification: EXOCYTOSIS
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2018-04-04 Released: 2019-04-17 
• Deposition Author(s): Sutton, R.B.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Engineering a C2-domain to bind PIP2

Evans, C.S., Lou, X., Bai, H., Rice, A.M., Salcido-Holguin, L., Rodriguez, E.N., Sutton, R.B., Chapman, E.R.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 14.69 kDa 
• Atom Count: 1,162 
• Modeled Residue Count: 127 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin 1 C2A beta4 chimera	A	128	Rattus norvegicus	Mutation(s): 0  Gene Names: Syt1 Membrane Entity: Yes
UniProt
Find proteins for P21707 (Rattus norvegicus) Explore P21707  Go to UniProtKB:  P21707

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.143	α = 90
b = 45.105	β = 90
c = 89.278	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Sutton, R.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	061876
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	063634

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description