7U4Q

Human Synaptotagmin-1 C2A Y181F Ca2+ bound

• PDB DOI: https://doi.org/10.2210/pdb7U4Q/pdb

• Classification: EXOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2022-02-28 Released: 2023-03-15 
• Deposition Author(s): Dominguez, M.J., Karmakar, S., Fuson, K.L., Sutton, R.B.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.189 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Human Synaptotagmin-1 C2A Y181F Ca2+ bound

Dominguez, M.J., Karmakar, S., Fuson, K.L., Sutton, R.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.71 kDa 
• Atom Count: 2,388 
• Modelled Residue Count: 252 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-1	A, B	133	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000067715

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.189 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.81	α = 90
b = 99.81	β = 90
c = 77.31	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
xia2	data reduction
xia2	data scaling
BUCCANEER	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Dominguez, M.J., Karmakar, S., Fuson, K.L., Sutton, R.B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	1R21MH070589-01

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description