[English] 日本語
Yorodumi
- PDB-5w5d: Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulated exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle-mediated transport in synapse / positive regulation of intracellular protein transport / 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 / regulation of vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / 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 / protein localization to membrane / clathrin-coated vesicle / syntaxin binding / presynaptic active zone / syntaxin-1 binding / insulin secretion / regulation of synaptic vesicle recycling / 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 / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / exocytosis / regulation of dopamine secretion / modulation of excitatory postsynaptic potential
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. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / Synaptobrevin-like / SNAP-25 family ...Synaphin / Synaphin protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

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

-
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 %

+
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