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- PDB-5w5d: Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C... -

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Basic information

Entry
Database: PDB / ID: 5w5d
TitleCrystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
Components
  • (Synaptosomal-associated protein ...) x 2
  • Complexin-1
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsEXOCYTOSIS / Prefusion primed complex / Neuronal Exocytosis / Synaptotagmin / SNARE complex / Complexin / synchronous neurotransmitter release
Function / homology
Function and homology information


regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of synaptic vesicle fusion to presynaptic active zone membrane / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion ...regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane / regulation of synaptic vesicle fusion to presynaptic active zone membrane / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / BLOC-1 complex / calcium-dependent activation of synaptic vesicle fusion / Lysosome Vesicle Biogenesis / myosin head/neck binding / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / zymogen granule membrane / storage vacuole / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / vesicle-mediated transport in synapse / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / regulation of establishment of protein localization / exocytic vesicle / positive regulation of intracellular protein transport / positive regulation of calcium ion-dependent exocytosis / vesicle organization / protein heterooligomerization / vesicle docking / ribbon synapse / positive regulation of dendrite extension / regulation of vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / secretion by cell / positive regulation of dopamine secretion / chloride channel inhibitor activity / SNAP receptor activity / SNARE complex / Clathrin-mediated endocytosis / vesicle fusion / calcium-ion regulated exocytosis / actomyosin / hormone secretion / LGI-ADAM interactions / dense core granule / Golgi to plasma membrane protein transport / calcium-dependent phospholipid binding / positive regulation of hormone secretion / neuron projection terminus / membraneless organelle assembly / ATP-dependent protein binding / neurotransmitter secretion / protein localization to membrane / syntaxin binding / clathrin-coated vesicle / presynaptic active zone / regulation of synaptic vesicle recycling / syntaxin-1 binding / insulin secretion / endosomal transport / Neutrophil degranulation / low-density lipoprotein particle receptor binding / clathrin binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / phosphatidylserine binding / neurotransmitter transport / regulation of synapse assembly / response to gravity / synaptic vesicle priming / myosin binding / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / exocytosis / associative learning
Similarity search - Function
Synaphin / Synaphin protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Synaptotagmin ...Synaphin / Synaphin protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Synaptotagmin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Complexin-1 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.496 Å
AuthorsZhou, Q. / Brunger, A.T.
CitationJournal: Nature / Year: 2017
Title: The primed SNARE-complexin-synaptotagmin complex for neuronal exocytosis.
Authors: Zhou, Q. / Zhou, P. / Wang, A.L. / Wu, D. / Zhao, M. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Complexin-1
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0337
Polymers56,0096
Non-polymers241
Water1,892105
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Complexin-1
F: Synaptotagmin-1
hetero molecules

A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Complexin-1
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,06614
Polymers112,01812
Non-polymers492
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)85.202, 89.199, 87.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11F-551-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Vesicle-associated membrane protein 2 / VAMP-2 / Synaptobrevin-2


Mass: 4704.220 Da / Num. of mol.: 1 / Fragment: UNP residues 29-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63045

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Protein , 3 types, 3 molecules BEF

#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7837.957 Da / Num. of mol.: 1 / Fragment: UNP residues 191-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#5: Protein Complexin-1 / Complexin I / CPX I / Synaphin-2


Mass: 9612.908 Da / Num. of mol.: 1 / Fragment: UNP residues 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cplx1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63041
#6: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 17352.201 Da / Num. of mol.: 1 / Fragment: UNP residues 270-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21707

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Synaptosomal-associated protein ... , 2 types, 2 molecules CD

#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 9030.114 Da / Num. of mol.: 1 / Fragment: UNP residues 7-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 7471.368 Da / Num. of mol.: 1 / Fragment: UNP residues 141-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli (E. coli) / References: UniProt: P60881

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Non-polymers , 2 types, 106 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH7.0, 15-17% PEG3350, 240 mM sodium malonate
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.496→44.5992 Å / Num. obs: 22138 / % possible obs: 93.2 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Χ2: 1.685 / Net I/σ(I): 17.4
Reflection shellResolution: 2.496→2.54 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 755 / CC1/2: 0.915 / Rpim(I) all: 0.16 / Χ2: 0.504 / % possible all: 66.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.53 Å44.6 Å
Translation5.53 Å44.6 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.22data extraction
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KIL, 3F04, 1UOW

1kil

3f04

1uow


Resolution: 2.496→44.599 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2312 1099 4.97 %
Rwork0.1981 --
obs0.1997 22138 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.65 Å2 / Biso mean: 69.461 Å2 / Biso min: 26.22 Å2
Refinement stepCycle: final / Resolution: 2.496→44.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 1 105 3206
Biso mean--73.11 61.03 -
Num. residues----406
LS refinement shellResolution: 2.496→2.943 Å
RfactorNum. reflection% reflection
Rfree0.2937 387 -
Rwork0.2545 --
obs-7116 82.41 %

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