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- PDB-5kj8: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long u... -

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Basic information

Entry
Database: PDB / ID: 5kj8
TitleStructure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction
Components
  • (Synaptosomal-associated protein ...) x 2
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 3
KeywordsENDOCYTOSIS / EXOCYTOSIS / XFEL STRUCTURE / SYNAPTIC FUSION COMPLEX / SYNAPTOTAGMIN1 / NEURONAL SNARE COMPLEX
Function / homology
Function and homology information


negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle ...negative regulation of secretion by cell / RHOF GTPase cycle / RHOB GTPase cycle / RHOD GTPase cycle / ER-Phagosome pathway / RAC2 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOQ GTPase cycle / RAC1 GTPase cycle / regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / Retrograde transport at the Trans-Golgi-Network / RHOA GTPase cycle / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / BLOC-1 complex / calcium-dependent activation of synaptic vesicle fusion / myosin head/neck binding / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / 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 / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / regulation of synaptic vesicle priming / regulated exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / regulation of establishment of protein localization / exocytic vesicle / positive regulation of calcium ion-dependent exocytosis / vesicle organization / protein heterooligomerization / ribbon synapse / positive regulation of dendrite extension / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / clathrin-coated vesicle membrane / secretion by cell / chloride channel inhibitor activity / Clathrin-mediated endocytosis / positive regulation of dopamine secretion / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / dense core granule / calcium-dependent phospholipid binding / positive regulation of hormone secretion / neuron projection terminus / membraneless organelle assembly / Golgi to plasma membrane protein transport / ATP-dependent protein binding / neurotransmitter secretion / retrograde transport, endosome to Golgi / protein localization to membrane / clathrin-coated vesicle / syntaxin binding / presynaptic active zone / syntaxin-1 binding / insulin secretion / endosomal transport / Neutrophil degranulation / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synapse assembly / neurotransmitter transport / SNARE complex assembly / positive regulation of neurotransmitter secretion / myosin binding / response to gravity / regulation of neuron projection development / intracellular vesicle / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / exocytosis / regulation of dopamine secretion
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. ...Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Synaptotagmin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å
AuthorsLyubimov, A.Y. / Uervirojnangkoorn, M. / Zhou, Q. / Zhao, M. / Sauter, N.K. / Brewster, A.S. / Weis, W.I. / Brunger, A.T.
CitationJournal: Elife / Year: 2016
Title: Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.
Authors: Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Zhou, Q. / Zhao, M. / Brewster, A.S. / Michels-Clark, T. / Holton, J.M. / Sauter, N.K. / Weis, W.I. / Brunger, A.T.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 3
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
G: Vesicle-associated membrane protein 3
H: Syntaxin-1A
I: Synaptosomal-associated protein 25
J: Synaptosomal-associated protein 25
K: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,56725
Polymers158,00611
Non-polymers56114
Water00
1
A: Vesicle-associated membrane protein 3
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,24911
Polymers63,0095
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1495
Polymers31,9891
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Vesicle-associated membrane protein 3
H: Syntaxin-1A
I: Synaptosomal-associated protein 25
J: Synaptosomal-associated protein 25
K: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1699
Polymers63,0095
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.790, 169.710, 286.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
35

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN G
112CHAIN B
212CHAIN H
113CHAIN C
213CHAIN I
114CHAIN D
214CHAIN J
115CHAIN E
215CHAIN F
315CHAIN K

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 3 types, 7 molecules AGBHEFK

#1: Protein Vesicle-associated membrane protein 3 / VAMP-3 / Cellubrevin / CEB / Synaptobrevin-3


Mass: 7231.061 Da / Num. of mol.: 2 / Fragment: UNP residues 14-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp3, Syb3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63025
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7706.761 Da / Num. of mol.: 2 / 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 Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 31988.838 Da / Num. of mol.: 3 / Fragment: UNP residues 141-419
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, 4 molecules CIDJ

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


Mass: 8741.725 Da / Num. of mol.: 2 / Fragment: UNP residues 9-83
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: 7340.173 Da / Num. of mol.: 2 / 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 , 1 types, 14 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca

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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: 5.3 Å3/Da / Density % sol: 76.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 27282 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 4.1→4.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.8 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S, 3F04, 1UOW

1n7s

3f04

1uow


Resolution: 4.1→49.64 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.25
RfactorNum. reflection% reflection
Rfree0.297 1333 4.99 %
Rwork0.283 --
obs0.284 26707 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 155 Å2
Refinement stepCycle: LAST / Resolution: 4.1→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10512 0 14 0 10526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211063
X-RAY DIFFRACTIONf_angle_d0.60714882
X-RAY DIFFRACTIONf_dihedral_angle_d10.3484246
X-RAY DIFFRACTIONf_chiral_restr0.0311656
X-RAY DIFFRACTIONf_plane_restr0.0031941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A580X-RAY DIFFRACTIONPOSITIONAL
12G580X-RAY DIFFRACTIONPOSITIONAL
21B570X-RAY DIFFRACTIONPOSITIONAL
22H570X-RAY DIFFRACTIONPOSITIONAL
31C634X-RAY DIFFRACTIONPOSITIONAL
32I634X-RAY DIFFRACTIONPOSITIONAL
41D560X-RAY DIFFRACTIONPOSITIONAL
42J560X-RAY DIFFRACTIONPOSITIONAL
51E3901X-RAY DIFFRACTIONPOSITIONAL
52F3901X-RAY DIFFRACTIONPOSITIONAL
53K3901X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1001-4.24650.40541320.38422519X-RAY DIFFRACTION99
4.2465-4.41650.32281320.3622494X-RAY DIFFRACTION99
4.4165-4.61730.33791330.33062535X-RAY DIFFRACTION99
4.6173-4.86060.36111300.32772477X-RAY DIFFRACTION98
4.8606-5.16480.33921310.31552493X-RAY DIFFRACTION98
5.1648-5.56310.37351340.32242556X-RAY DIFFRACTION99
5.5631-6.1220.35421340.33972554X-RAY DIFFRACTION99
6.122-7.00580.31591340.31312541X-RAY DIFFRACTION98
7.0058-8.81850.27761350.25032563X-RAY DIFFRACTION97
8.8185-49.64150.19951380.19852642X-RAY DIFFRACTION95

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