[English] 日本語
Yorodumi
- PDB-2m8r: Pre-Fusion Solution NMR Structure of Neuronal SNARE Syntaxin 1A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m8r
TitlePre-Fusion Solution NMR Structure of Neuronal SNARE Syntaxin 1A
ComponentsSyntaxin-1A
KeywordsMEMBRANE PROTEIN / syntaxin / SNARE / Prefusion
Function / homology
Function and homology information


myosin head/neck binding / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / positive regulation of norepinephrine secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion ...myosin head/neck binding / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / positive regulation of norepinephrine secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / response to gravity / positive regulation of calcium ion-dependent exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / vesicle docking / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / regulation of exocytosis / LGI-ADAM interactions / calcium-ion regulated exocytosis / hormone secretion / actomyosin / protein localization to membrane / ATP-dependent protein binding / insulin secretion / neurotransmitter transport / SNARE complex assembly / positive regulation of neurotransmitter secretion / myosin binding / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / exocytosis / synaptic vesicle exocytosis / protein sumoylation / positive regulation of excitatory postsynaptic potential / synaptic vesicle endocytosis / endomembrane system / calcium channel inhibitor activity / presynaptic active zone membrane / acrosomal vesicle / SNARE binding / secretory granule / intracellular protein transport / postsynaptic density membrane / Schaffer collateral - CA1 synapse / kinase binding / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / presynapse / presynaptic membrane / protein-macromolecule adaptor activity / nuclear membrane / transmembrane transporter binding / postsynaptic density / neuron projection / axon / glutamatergic synapse / synapse / protein-containing complex binding / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model20
AuthorsLiang, B. / Kiessling, V. / Tamm, L.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate.
Authors: Liang, B. / Kiessling, V. / Tamm, L.K.
History
DepositionMay 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Syntaxin-1A


Theoretical massNumber of molelcules
Total (without water)12,3341
Polymers12,3341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #20lowest energy

-
Components

#1: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 12334.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HN(CO)CA
1723D HNHA
1823D (H)CCH-TOCSY
1923D (H)CCH-COSY
11023D H(CCO)NH
11123D C(CO)NH
11222D 1H-13C HSQC aromatic
11322D 1H-13C HSQC aliphatic
11423D 1H-15N NOESY
11523D 1H-13C NOESY
11613D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] syntaxin, 100 mM DPC, 10 mM HEPES, 10 mM MES, 10 mM sodium acetate, 150 mM sodium chloride, 5 mM DTT, 1 mM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] syntaxin, 100 mM [U-99% 2H] DPC, 150 mM sodium chloride, 0.02 % sodium azide, 10 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-13C; U-15N; U-2H]1
100 mMDPC-21
10 mMHEPES-31
10 mMMES-41
10 mMsodium acetate-51
150 mMsodium chloride-61
5 mMDTT-71
1 mMEDTA-81
1 mMentity-9[U-100% 13C; U-100% 15N]2
100 mMDPC-10[U-99% 2H]2
150 mMsodium chloride-112
0.02 %sodium azide-122
10 mMsodium phosphate-132
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 313 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1085 / NOE intraresidue total count: 512 / NOE long range total count: 6 / NOE medium range total count: 218 / NOE sequential total count: 349 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 34 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.033 Å / Distance rms dev error: 0.002 Å

+
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