3HD7 Exocytosis date May 07, 2009
title Helical Extension Of The Neuronal Snare Complex Into The Mem Spacegroup C 1 2 1
authors A.Stein, G.Weber, M.C.Wahl, R.Jahn
compound source
Molecule: Vesicle-Associated Membrane Protein 2
Chain: A, E
Fragment: C-Terminal Fragment, Unp Residues 30-116
Synonym: Vamp-2, Synaptobrevin-2
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Vamp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Syntaxin-1a
Chain: B, F
Fragment: C-Terminal Fragment, Unp Residues 183-288
Synonym: Synaptotagmin-Associated 35 Kda Protein, P35a, Neu Specific Antigen Hpc-1;
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Stx1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Synaptosomal-Associated Protein 25
Chain: C, G
Fragment: N-Terminal Fragment, Unp Residues 7-83
Synonym: Snap-25, Synaptosomal-Associated 25 Kda Protein, S Protein, Sup;
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Snap25
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Synaptosomal-Associated Protein 25
Chain: D, H
Fragment: C-Terminal Fragment, Unp Residues 141-204
Synonym: Snap-25, Synaptosomal-Associated 25 Kda Protein, S Protein, Sup;
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Snap25
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: C 1 2 1
R_factor 0.239 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
265.412 135.490 58.689 90.00 96.34 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand GGG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B


H, C, D, G


Primary referenceHelical extension of the neuronal SNARE complex into the membrane., Stein A, Weber G, Wahl MC, Jahn R, Nature. 2009 Jul 1. PMID:19571812
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (235 Kb) [Save to disk]
  • Biological Unit Coordinates (3hd7.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (3hd7.pdb2.gz) 115 Kb
  • LPC: Ligand-Protein Contacts for 3HD7
  • CSU: Contacts of Structural Units for 3HD7
  • Likely Quarternary Molecular Structure file(s) for 3HD7
  • Structure Factors (441 Kb)
  • Retrieve 3HD7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HD7 from S2C, [Save to disk]
  • Re-refined 3hd7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HD7 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3HD7
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3HD7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hd7_E] [3hd7_D] [3hd7_C] [3hd7_F] [3hd7_A] [3hd7_H] [3hd7_G] [3hd7] [3hd7_B]
  • SWISS-PROT database: [P60881] [P32851] [P63045]
  • Domain organization of [SNP25_RAT] [STX1A_RAT] [VAMP2_RAT] by SWISSPFAM
  • Domain found in 3HD7: [t_SNARE ] by SMART
  • Other resources with information on 3HD7
  • Community annotation for 3HD7 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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