[English] 日本語
Yorodumi
- PDB-5kj8: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long u... -

+
Open data


ID or keywords:

Loading...

-
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 / Retrograde transport at the Trans-Golgi-Network / RHOQ 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 / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle / RAC1 GTPase cycle / BLOC-1 complex / regulation of vesicle fusion / 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 / RHOA GTPase cycle / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / regulation of regulated secretory pathway / 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 / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / dense core granule / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / synaptic vesicle docking / regulation of synaptic vesicle priming / regulation of establishment of protein localization / ribbon synapse / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to gravity / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / positive regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / regulation of exocytosis / secretion by cell / SNAP receptor activity / SNARE complex / chloride channel inhibitor activity / vesicle organization / protein heterooligomerization / clathrin-coated vesicle membrane / vesicle fusion / positive regulation of dopamine secretion / calcium-ion regulated exocytosis / Cargo recognition for clathrin-mediated endocytosis / LGI-ADAM interactions / Clathrin-mediated endocytosis / actomyosin / hormone secretion / Golgi to plasma membrane protein transport / positive regulation of dendrite extension / positive regulation of hormone secretion / neurotransmitter secretion / ATP-dependent protein binding / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / retrograde transport, endosome to Golgi / protein localization to membrane / syntaxin binding / syntaxin-1 binding / clathrin-coated vesicle / insulin secretion / endosomal transport / Neutrophil degranulation / SNARE complex assembly / positive regulation of neurotransmitter secretion / clathrin binding / neurotransmitter transport / low-density lipoprotein particle receptor binding / synaptic vesicle priming / regulation of synapse assembly / regulation of synaptic vesicle exocytosis / phosphatidylserine binding / myosin binding / positive regulation of receptor recycling / regulation of neuron projection development / intracellular vesicle / regulation of dopamine secretion / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more