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- PDB-1urq: Crystal structure of neuronal Q-SNAREs in complex with R-SNARE mo... -

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Basic information

Entry
Database: PDB / ID: 1urq
TitleCrystal structure of neuronal Q-SNAREs in complex with R-SNARE motif of Tomosyn
Components
  • (SYNAPTOSOMAL-ASSOCIATED PROTEIN 25) x 2
  • M-TOMOSYN ISOFORM
  • SYNTAXIN 1A
KeywordsTRANSPORT PROTEIN / TOMOSYN-SNARE COMPLEX / EXOCYTOSIS / FOUR HELICAL BUNDLE / COILED COIL
Function / homology
Function and homology information


extrinsic component of neuronal dense core vesicle membrane / small GTPase binding => GO:0031267 / BLOC-1 complex / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex ...extrinsic component of neuronal dense core vesicle membrane / small GTPase binding => GO:0031267 / BLOC-1 complex / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle fusion / vesicle docking / acetylcholine-gated channel complex / positive regulation of calcium ion-dependent exocytosis / myosin II binding / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neurotransmitter transport / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / regulation of synaptic vesicle exocytosis / myosin binding / regulation of protein secretion / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / long-term memory / axonal growth cone / presynaptic active zone membrane / voltage-gated potassium channel complex / extrinsic component of cytoplasmic side of plasma membrane / somatodendritic compartment / hippocampal mossy fiber to CA3 synapse / photoreceptor inner segment / axonogenesis / GTPase activator activity / SNARE binding / acrosomal vesicle / secretory granule / filopodium / locomotory behavior / long-term synaptic potentiation / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / neuron differentiation / trans-Golgi network / positive regulation of insulin secretion / terminal bouton / synaptic vesicle membrane / kinase binding / calcium-dependent protein binding / protein transport / actin cytoskeleton
Similarity search - Function
Lethal giant larvae (Lgl)-like, C-terminal domain / Lethal giant larvae(Lgl) like, C-terminal / Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin ...Lethal giant larvae (Lgl)-like, C-terminal domain / Lethal giant larvae(Lgl) like, C-terminal / Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / : / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Synaptosomal-associated protein 25 / Syntaxin-1A / Synaptosomal-associated protein 25 / Syntaxin-binding protein 5 / Syntaxin-binding protein 5
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPobbati, A. / Razeto, A. / Becker, S. / Fasshauer, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for the Inhibitory Role of Tomosyn in Exocytosis
Authors: Pobbati, A. / Razeto, A. / Boddener, M. / Becker, S. / Fasshauer, D.
History
DepositionOct 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M-TOMOSYN ISOFORM
B: SYNTAXIN 1A
C: SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
D: SYNAPTOSOMAL-ASSOCIATED PROTEIN 25


Theoretical massNumber of molelcules
Total (without water)32,5524
Polymers32,5524
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.054, 35.602, 93.541
Angle α, β, γ (deg.)90.00, 132.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein M-TOMOSYN ISOFORM


Mass: 6686.593 Da / Num. of mol.: 1 / Fragment: RESIDUES 1050-1109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell: NEURON / Organ: BRAIN / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z152, UniProt: Q9WU70*PLUS
#2: Protein SYNTAXIN 1A / SYNAPTOTAGMIN ASSOCIATED 35 KDA PROTEIN / P35A / NEURON-SPECIFIC ANTIGEN HPC-1


Mass: 8711.805 Da / Num. of mol.: 1 / Fragment: T-SNARE COILED-COIL HOMOLOGY, RESIDUES 188-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell: NEURON / Organ: BRAIN / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851
#3: Protein SYNAPTOSOMAL-ASSOCIATED PROTEIN 25 / SNAP-25A / SUPER PROTEIN / SUP


Mass: 9312.390 Da / Num. of mol.: 1 / Fragment: T-SNARE COILED-COIL HOMOLOGY 1, RESIDUES 7-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell: NEURON / Organ: BRAIN / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13795, UniProt: P60881*PLUS
#4: Protein SYNAPTOSOMAL-ASSOCIATED PROTEIN 25 / SNAP-25A / SUPER PROTEIN / SUP


Mass: 7840.723 Da / Num. of mol.: 1 / Fragment: T-SNARE COILED-COIL HOMOLOGY 2, RESIDUES 141-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell: NEURON / Organ: BRAIN / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13795, UniProt: P60881*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN DOCKING OF SYNAPTIC VESICLES AT PRESYNAPTIC ACTIVE ZONES. PLAYS A CRITICAL ROLE IN ...INVOLVED IN DOCKING OF SYNAPTIC VESICLES AT PRESYNAPTIC ACTIVE ZONES. PLAYS A CRITICAL ROLE IN NEUROTRANSMITTER EXOCYTOSIS. TSNARE INVOLVED IN THE MOLECULAR REGULATION OF NEUROTRANSMITTER RELEASE. PLAYS AN IMPORTANT ROLE IN THE SYNAPTIC FUNCTION OF SPECIFIC NEURONAL SYSTEMS. ASSOCIATES WITH PROTEINS INVOLVED IN VESICLE DOCKING AND MEMBRANE FUSION.
Sequence detailsTHE CONFLICTS THAT ARE SHOWN FOR CHAIN C IN THE DBREF ARISE DUE TO A VARIABE SPLICED ISOFORM OF ...THE CONFLICTS THAT ARE SHOWN FOR CHAIN C IN THE DBREF ARISE DUE TO A VARIABE SPLICED ISOFORM OF P13795. THE VARSPLIC ID FOR THIS IS VSP_006186 AND IS ACCESSIBLE FROM THE FOLLOWING WEB ADDRESS: HTTP://SRS.EBI.AC.UK/SRSBIN/CGI-BIN/WGETZ?-E+ [SWALL_FEATURES-ID:SN25_HUMAN_5]

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 48.9 %
Crystal growpH: 6 / Details: 30% MPD, 50MM CACL2, 50MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
Details: PREMIRROR, DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR, BENT MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→19.39 Å / Num. obs: 21027 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.08429 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6.4 / % possible all: 97.1

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N7S

1n7s


Resolution: 2→19.3892 Å / SU B: 2.209 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.1529 / ESU R Free: 0.1538
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 1077 5.12 %RANDOM
Rwork0.1653 ---
obs0.1661 19950 99.5 %-
Displacement parametersBiso mean: 30.6 Å2
Refinement stepCycle: LAST / Resolution: 2→19.3892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 278 2183

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