1EPU

X-RAY crystal structure of neuronal SEC1 from squid

PDB DOI: https://doi.org/10.2210/pdb1EPU/pdb

Classification: ENDOCYTOSIS/EXOCYTOSIS
Organism(s): Doryteuthis pealeii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-03-29 Released: 2000-08-09
Deposition Author(s): Bracher, A., Perrakis, A., Dresbach, T., Betz, H., Weissenhorn, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.277
R-Value Work: 0.240
R-Value Observed: 0.251

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis.

Bracher, A., Perrakis, A., Dresbach, T., Betz, H., Weissenhorn, W.

(2000) Structure 8: 685-694

PubMed: 10903948 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(00)00156-8
Primary Citation of Related Structures:
1EPU

PubMed Abstract:
Sec1-like molecules have been implicated in a variety of eukaryotic vesicle transport processes including neurotransmitter release by exocytosis. They regulate vesicle transport by binding to a t-SNARE from the syntaxin family. This process is thought to prevent SNARE complex formation, a protein complex required for membrane fusion. Whereas Sec1 molecules are essential for neurotransmitter release and other secretory events, their interaction with syntaxin molecules seems to represent a negative regulatory step in secretion.

Organizational Affiliation

European Molecular Biology Laboratory (EMBL), Grenoble, 38000, France.

Macromolecule Content

Total Structure Weight: 68.82 kDa
Atom Count: 4,481
Modelled Residue Count: 546
Deposited Residue Count: 591
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-SEC1	A	591	Doryteuthis pealeii	Mutation(s): 0
UniProt
Find proteins for O62547 (Doryteuthis pealeii) Explore O62547 Go to UniProtKB: O62547
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O62547
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.277
R-Value Work: 0.240
R-Value Observed: 0.251
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.063	α = 90
b = 121.989	β = 104.53
c = 69.046	γ = 90

Software Package:

Software Name	Purpose
SnB	phasing
SHARP	phasing
DMMulti	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DMMulti	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2000-08-09

Deposition Author(s):

Weissenhorn, W.

Revision History (Full details and data files)

Version 1.0: 2000-08-09
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-07-27
Changes: Atomic model, Data collection
Version 1.4: 2017-10-04
Changes: Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.