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- PDB-5cci: Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short ... -

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Basic information

Entry
Database: PDB / ID: 5cci
TitleStructure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form)
Components
  • (Synaptosomal-associated protein ...) x 2
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsENDOCYTOSIS / EXOCYTOSIS / synaptic fusion complex / Synaptotagmin1 / neuronal SNARE complex
Function / homology
Function and homology information


trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / Other interleukin signaling / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / regulation of regulated secretory pathway / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / calcium-dependent activation of synaptic vesicle fusion / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Lysosome Vesicle Biogenesis / regulated exocytosis / presynaptic dense core vesicle exocytosis / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / dense core granule / zymogen granule membrane / extrinsic component of presynaptic membrane / ribbon synapse / synaptic vesicle docking / regulation of synaptic vesicle priming / Golgi Associated Vesicle Biogenesis / storage vacuole / regulation of establishment of protein localization / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to gravity / positive regulation of calcium ion-dependent exocytosis / vesicle-mediated transport in synapse / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / vesicle docking / eosinophil degranulation / exocytic vesicle / secretion by cell / SNAP receptor activity / chloride channel inhibitor activity / regulation of exocytosis / SNARE complex / vesicle organization / vesicle fusion / neurotransmitter receptor internalization / protein heterooligomerization / regulation of vesicle-mediated transport / positive regulation of dopamine secretion / Cargo recognition for clathrin-mediated endocytosis / calcium-ion regulated exocytosis / LGI-ADAM interactions / Clathrin-mediated endocytosis / actomyosin / hormone secretion / positive regulation of intracellular protein transport / positive regulation of dendrite extension / Golgi to plasma membrane protein transport / positive regulation of hormone secretion / neurotransmitter secretion / ATP-dependent protein binding / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / protein localization to membrane / syntaxin binding / regulation of synaptic vesicle recycling / syntaxin-1 binding / clathrin-coated vesicle / insulin secretion / SNARE complex assembly / endosomal transport / Neutrophil degranulation / positive regulation of neurotransmitter secretion / neurotransmitter transport / clathrin binding / synaptic vesicle priming / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle exocytosis / myosin binding / regulation of synapse assembly / phosphatidylserine binding / regulation of neuron projection development / regulation of dopamine secretion / exocytosis / modulation of excitatory postsynaptic potential / associative learning / synaptic vesicle exocytosis
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Synaptobrevin-like ...Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Synaptobrevin-like / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Synaptotagmin / 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 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å
AuthorsZhou, Q. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Weis, W.I. / Brunger, A.T.
CitationJournal: Nature / Year: 2015
Title: Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis.
Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. ...Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. / Lemke, H.T. / Pfuetzner, R.A. / Choi, U.B. / Weis, W.I. / Diao, J. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Derived calculations
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Synaptotagmin-1
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,16210
Polymers96,0656
Non-polymers974
Water00
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
hetero molecules

F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,45813
Polymers128,3127
Non-polymers1466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)69.064, 171.759, 146.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN E
211CHAIN F
DetailsAuthors state that the biological assembly includes Chain A, B, C, D, Chain E 273-421, Chain F 273-421, Chain F 141-265 from symmetric neighbor.

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Components

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Protein , 3 types, 4 molecules ABEF

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


Mass: 7231.061 Da / Num. of mol.: 1 / Fragment: UNP residues 28-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63045
#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 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851
#5: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 32247.197 Da / Num. of mol.: 2 / Fragment: UNP residues 141-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881

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Non-polymers , 1 types, 4 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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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: 4.55 Å3/Da / Density % sol: 72.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.75% v/v PEG3350, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2

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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: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.996→146.561 Å / Num. obs: 15069 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 133.6 Å2 / Rsym value: 0.119 / Net I/σ(I): 8
Reflection shellResolution: 4→4.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 0.7 / Rsym value: 1.05 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S,3F04,1UOW

1n7s

3f04

1uow


Resolution: 4.1→48.24 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 38.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.323 1283 5.08 %
Rwork0.276 --
obs0.279 25275 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 193.4 Å2
Refinement stepCycle: LAST / Resolution: 4.1→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 4 0 6406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036613
X-RAY DIFFRACTIONf_angle_d0.7148905
X-RAY DIFFRACTIONf_dihedral_angle_d10.492517
X-RAY DIFFRACTIONf_chiral_restr0.032993
X-RAY DIFFRACTIONf_plane_restr0.0021157
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11E2280X-RAY DIFFRACTIONPOSITIONAL
12F2280X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.26410.44341360.3982706X-RAY DIFFRACTION97
4.2641-4.4580.34071720.35562672X-RAY DIFFRACTION98
4.458-4.69290.32881220.32162755X-RAY DIFFRACTION98
4.6929-4.98660.40381480.30882691X-RAY DIFFRACTION97
4.9866-5.37120.34731400.30312645X-RAY DIFFRACTION95
5.3712-5.91080.33751390.32732665X-RAY DIFFRACTION96
5.9108-6.76410.31671540.30792681X-RAY DIFFRACTION97
6.7641-8.51450.37161330.25122612X-RAY DIFFRACTION93
8.5145-48.24070.23551390.19532565X-RAY DIFFRACTION92

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