3B5N | pdb_00003b5n

Structure of the yeast plasma membrane SNARE complex

PDB DOI: https://doi.org/10.2210/pdb3B5N/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-10-26 Released: 2007-11-20
Deposition Author(s): Strop, P., Brunger, A.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.248 (Depositor), 0.249 (DCC)
R-Value Work:
0.206 (Depositor), 0.209 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Structure of the Yeast Plasma Membrane SNARE Complex Reveals Destabilizing Water-filled Cavities.

Strop, P., Kaiser, S.E., Vrljic, M., Brunger, A.T.

(2008) J Biological Chem 283: 1113-1119

PubMed: 17956869 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M707912200
Primary Citation Related Structures:
3B5N

PubMed Abstract:
SNARE proteins form a complex that leads to membrane fusion between vesicles, organelles, and plasma membrane in all eukaryotic cells. We report the 1.7A resolution structure of the SNARE complex that mediates exocytosis at the plasma membrane in the yeast Saccharomyces cerevisiae. Similar to its neuronal and endosomal homologues, the S. cerevisiae SNARE complex forms a parallel four-helix bundle in the center of which is an ionic layer. The S. cerevisiae SNARE complex exhibits increased helix bending near the ionic layer, contains water-filled cavities in the complex core, and exhibits reduced thermal stability relative to mammalian SNARE complexes. Mutagenesis experiments suggest that the water-filled cavities contribute to the lower stability of the S. cerevisiae complex.

Organizational Affiliation

Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA.

Macromolecule Content

Total Structure Weight: 88.81 kDa
Atom Count: 6,656
Modeled Residue Count: 771
Deposited Residue Count: 792
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptobrevin homolog 1	A, E, I	61	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SNC1
UniProt
Find proteins for P31109 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31109 Go to UniProtKB: P31109
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31109
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SSO1	B, F, J	69	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SSO1
UniProt
Find proteins for P32867 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32867 Go to UniProtKB: P32867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32867
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein SEC9	C, G, K	70	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SEC9, HSS7
UniProt
Find proteins for P40357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40357 Go to UniProtKB: P40357
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40357
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein SEC9	D, H, L	64	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SEC9, HSS7
UniProt
Find proteins for P40357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40357 Go to UniProtKB: P40357
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40357
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.248 (Depositor), 0.249 (DCC)
R-Value Work: 0.206 (Depositor), 0.209 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.956	α = 90
b = 48.113	β = 97.77
c = 110.265	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Strop, P.

Brunger, A.T.

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description