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

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Basic information

Entry
Database: PDB / ID: 5ccg
TitleStructure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form)
Components
  • (Synaptosomal-associated protein ...) x 2
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsENDOCYTOSIS / EXOCYTOSIS / XFEL structure / synaptic fusion complex / Synaptotagmin1 / neuronal SNARE complex
Function / homology
Function and homology information


trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / 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 / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / 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 / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / calcium ion sensor activity / regulation of regulated secretory pathway / 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 / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / 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 / zymogen granule membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / vesicle fusion / regulation of calcium ion-dependent exocytosis / vesicle docking / positive regulation of calcium ion-dependent exocytosis / exocytic vesicle / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / positive regulation of dendrite extension / Golgi to plasma membrane protein transport / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / myosin binding / regulation of dopamine secretion / phosphatidylserine binding / 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
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / 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 / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZhou, Q. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / 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: Data collection / Database references
Revision 1.2Sep 9, 2015Group: Derived calculations
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.6Sep 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 / 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 / _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 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
G: Vesicle-associated membrane protein 2
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)160,64430
Polymers159,88311
Non-polymers76119
Water32418
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)129,03325
Polymers128,3127
Non-polymers72118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
2
G: Vesicle-associated membrane protein 2
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)64,01810
Polymers63,8185
Non-polymers2005
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.603, 171.092, 291.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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, 7 molecules AGBHEFK

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


Mass: 7231.061 Da / Num. of mol.: 2 / 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.: 2 / 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.: 3 / 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, 4 molecules CIDJ

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


Mass: 9030.114 Da / Num. of mol.: 2 / 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.: 2 / 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 , 2 types, 37 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 72

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Sample preparation

CrystalDensity Matthews: 5.56 Å3/Da / Density % sol: 77.71 %
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: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.3 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 39174 / % possible obs: 87.6 % / Redundancy: 5 % / CC1/2: 0.927 / Rmerge(I) obs: 0.397 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.355 / % possible all: 65.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
cctbx.xfeldata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S,3F04,1UOW

1n7s

3f04

1uow


Resolution: 3.5→19.972 Å / SU ML: 0.88 / Cross valid method: FREE R-VALUE / σ(F): 1.84 / Phase error: 38.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3525 1999 5.1 %
Rwork0.3218 --
obs0.3233 39171 87.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→19.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10538 0 19 18 10575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311051
X-RAY DIFFRACTIONf_angle_d0.75814870
X-RAY DIFFRACTIONf_dihedral_angle_d10.7354232
X-RAY DIFFRACTIONf_chiral_restr0.0411656
X-RAY DIFFRACTIONf_plane_restr0.0051941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.58710.41091000.42561853X-RAY DIFFRACTION63
3.5871-3.68350.39771200.412235X-RAY DIFFRACTION74
3.6835-3.79110.4411220.39412271X-RAY DIFFRACTION76
3.7911-3.91260.42051270.3842375X-RAY DIFFRACTION79
3.9126-4.05140.38551310.36752439X-RAY DIFFRACTION82
4.0514-4.21210.41641390.35132560X-RAY DIFFRACTION85
4.2121-4.40190.39751450.33682693X-RAY DIFFRACTION89
4.4019-4.63120.33731500.31762801X-RAY DIFFRACTION92
4.6312-4.91730.37361530.30062845X-RAY DIFFRACTION95
4.9173-5.29040.31551570.29772913X-RAY DIFFRACTION96
5.2904-5.81090.31521580.30352951X-RAY DIFFRACTION97
5.8109-6.62470.33131600.30792962X-RAY DIFFRACTION97
6.6247-8.24750.32271650.28173065X-RAY DIFFRACTION99
8.2475-19.97210.25681720.23093209X-RAY DIFFRACTION99

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