1N7S | pdb_00001n7s

High Resolution Structure of a Truncated Neuronal SNARE Complex

PDB DOI: https://doi.org/10.2210/pdb1N7S/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-11-16 Released: 2002-12-27
Deposition Author(s): Ernst, J.A., Brunger, A.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

High Resolution Structure, Stability, and Synaptotagmin Binding of a Truncated Neuronal SNARE Complex

Ernst, J.A., Brunger, A.T.

(2003) J Biological Chem 278: 8630-8636

PubMed: 12496247 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M211889200
Primary Citation Related Structures:
1N7S

PubMed Abstract:
The structure of a truncated SNARE complex has been solved to 1.4-A resolution revealing a stabilizing salt bridge, sites of hydration, and conformational variability of the ionic central layer that were not observed in a previously published structure at 2.4-A resolution (Sutton, R. B., Fasshauer, D., Jahn, R., and Brunger, A. T. (1998) Nature 395, 347-353). The truncated complex lacks residues involved in phospholipid binding and denatures at a lower temperature than longer complexes as assessed by SDS and circular dichroism thermal melts. The truncated SNARE complex is monomeric, and it retains binding to synaptotagmin I.

Organizational Affiliation

Howard Hughes Medical Institute, Stanford University, California 94305, USA.

Macromolecule Content

Total Structure Weight: 32.1 kDa
Atom Count: 2,547
Modeled Residue Count: 276
Deposited Residue Count: 276
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vesicle-associated membrane protein 2	A	63	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P63045 (Rattus norvegicus) Explore P63045 Go to UniProtKB: P63045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63045
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntaxin 1A	B	68	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P32851 (Rattus norvegicus) Explore P32851 Go to UniProtKB: P32851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32851
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SNAP-25A	C	79	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P60881 (Rattus norvegicus) Explore P60881 Go to UniProtKB: P60881
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60881
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SNAP-25A	D	66	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P60881 (Rattus norvegicus) Explore P60881 Go to UniProtKB: P60881
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain E [auth A]	E [auth A], G [auth C], H [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.224 (Depositor), 0.223 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.767	α = 90
b = 51.75	β = 90
c = 132.938	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-12-27

Deposition Author(s):

Ernst, J.A.

Brunger, A.T.

Revision History (Full details and data files)

Version 1.0: 2002-12-27
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-31
Changes: Experimental preparation
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description