Macromolecule Content

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

7U4Q

Human Synaptotagmin-1 C2A Y181F Ca2+ bound

PDB DOI: 10.2210/pdb7U4Q/pdb

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

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human Synaptotagmin-1 C2A Y181F Ca2+ bound

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

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens) Explore P21579 Go to UniProtKB: P21579
PHAROS: P21579
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21579
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Dominguez, M.J.

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

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.