7TUA

Human Synaptotagmin-1 C2B Y312F without Ca2+

PDB DOI: https://doi.org/10.2210/pdb7TUA/pdb

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

Deposited: 2022-02-02 Released: 2023-03-22
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: 1.35 Å
R-Value Free: 0.199
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Human Synaptotagmin-1 C2B Y312F without Ca2+

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

To be published.

Macromolecule Content

Total Structure Weight: 17.96 kDa
Atom Count: 1,484
Modelled Residue Count: 148
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin	A	157	Homo sapiens	Mutation(s): 0 Gene Names: SYT1, hCG_2016754 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21579
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.199
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.44	α = 90
b = 54.44	β = 90
c = 104.07	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB-REDO	refinement
xia2	data scaling
xia2	data reduction
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-22

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: 2023-03-22
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

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.