[English] 日本語
Yorodumi
- PDB-1n7s: High Resolution Structure of a Truncated Neuronal SNARE Complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1n7s
TitleHigh Resolution Structure of a Truncated Neuronal SNARE Complex
Components
  • (SNAP-25A) x 2
  • Syntaxin 1ASTX1A
  • vesicle-associated membrane protein 2Vesicle-associated membrane protein
KeywordsTRANSPORT PROTEIN / neuronal SNARE protein complex / four helix bundle / Transport protein
Function / homologySynaptosomal-associated protein 25 / Syntaxin / v-SNARE coiled-coil homology domain profile. / t-SNARE coiled-coil homology domain profile. / Synaptobrevin signature. / SNARE domain / Synaptobrevin / SNAP-25 family / Vesicle-associated membrane protein 2 / Norepinephrine Neurotransmitter Release Cycle ...Synaptosomal-associated protein 25 / Syntaxin / v-SNARE coiled-coil homology domain profile. / t-SNARE coiled-coil homology domain profile. / Synaptobrevin signature. / SNARE domain / Synaptobrevin / SNAP-25 family / Vesicle-associated membrane protein 2 / Norepinephrine Neurotransmitter Release Cycle / Syntaxin 1A / Synaptobrevin/Vesicle-associated membrane protein / SNARE / Syntaxin/epimorphin, conserved site / Syntaxin, N-terminal domain / Synaptobrevin / SNAP-25 / Serotonin Neurotransmitter Release Cycle / Syntaxin / epimorphin family signature. / Glutamate Neurotransmitter Release Cycle / Clathrin derived vesicle budding / GABA synthesis, release, reuptake and degradation / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / LGI-ADAM interactions / Other interleukin signaling / Golgi Associated Vesicle Biogenesis / Dopamine Neurotransmitter Release Cycle / Lysosome Vesicle Biogenesis / Target SNARE coiled-coil homology domain / Acetylcholine Neurotransmitter Release Cycle / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / storage vacuole / myosin head/neck binding / regulation of synaptic vesicle priming / anchored component of presynaptic membrane / zymogen granule membrane / growth hormone secretion / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / neurotransmitter transport / positive regulation of norepinephrine secretion / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / presynaptic active zone membrane / synaptic vesicle fusion to presynaptic active zone membrane / positive regulation of catecholamine secretion / synaptic vesicle docking / SNARE complex assembly / regulation of synaptic vesicle recycling / synaptic vesicle priming / intracellular organelle / positive regulation of neurotransmitter secretion / positive regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / regulation of synapse assembly / vesicle docking / protein localization to membrane / Golgi to plasma membrane protein transport / chloride channel inhibitor activity / vesicle fusion / integral component of synaptic vesicle membrane / response to gravity / positive regulation of hormone secretion / SNAP receptor activity / sleep / regulation of exocytosis / synaptic vesicle exocytosis / regulation of neuron projection development / SNARE complex / positive regulation of intracellular protein transport / syntaxin-1 binding / ATP-dependent protein binding / neuron projection terminus / actomyosin / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / myosin binding / clathrin-coated vesicle / syntaxin binding / calcium channel inhibitor activity / voltage-gated potassium channel activity / exocytosis / endomembrane system / long-term memory / positive regulation of insulin secretion / SNARE binding / positive regulation of excitatory postsynaptic potential / voltage-gated potassium channel complex / axonal growth cone / axonogenesis / long-term synaptic potentiation / secretory granule / vesicle-mediated transport / filopodium / endosomal transport / response to glucose / synaptic vesicle membrane / neuron differentiation / integral component of presynaptic membrane
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.45 Å resolution
AuthorsErnst, J.A. / Brunger, A.T.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: High Resolution Structure, Stability, and Synaptotagmin Binding of a Truncated Neuronal SNARE Complex
Authors: Ernst, J.A. / Brunger, A.T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 16, 2002 / Release: Dec 27, 2002
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2002Structure modelrepositoryInitial release
1.1Apr 28, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 31, 2018Structure modelExperimental preparationexptl_crystal_grow_exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: vesicle-associated membrane protein 2
B: Syntaxin 1A
C: SNAP-25A
D: SNAP-25A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0979
Polyers31,7404
Non-polymers3575
Water5,801322
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)12500
ΔGint (kcal/M)-140
Surface area (Å2)15120
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)39.767, 51.750, 132.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

-
Components

-
Protein/peptide , 4 types, 4 molecules ABCD

#1: Protein/peptide vesicle-associated membrane protein 2 / Vesicle-associated membrane protein / Synaptobrevin 2 (vesicle-associated membrane protein / VAMP-2)


Mass: 7231.061 Da / Num. of mol.: 1 / Fragment: SBc / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: Rattus / Plasmid name: pET28a / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63045
#2: Protein/peptide Syntaxin 1A / STX1A / Synaptotagmin associated 35 kDa protein / P35A / Neuron-specific antigen HPC-1


Mass: 7850.891 Da / Num. of mol.: 1 / Fragment: SXc / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: Rattus / Plasmid name: pET28a / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32851
#3: Protein/peptide SNAP-25A


Mass: 9174.243 Da / Num. of mol.: 1 / Fragment: SN1b / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: Rattus / Plasmid name: pET28a / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60881
#4: Protein/peptide SNAP-25A


Mass: 7484.302 Da / Num. of mol.: 1 / Fragment: SN2c / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: Rattus / Plasmid name: pET28a / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60881

-
Non-polymers , 3 types, 327 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Formula: Ca / Calcium
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 / Density percent sol: 35.37 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, CaCl2, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K
Crystal grow
*PLUS
Temp: 4 and 20 ℃ / pH: 7.8
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
19 mg/mlproteindrop
2200 mMdropNaCl
310 mMHEPESdroppH7.8
45 mMdithiothreitoldrop
515-20 %MPDreservoir
675-125 mMreservoirCaCl2
750 mMMESreservoirpH5.0-6.0

-
Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.2.1 / Synchrotron site: ALS / Beamline: 8.2.1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Sep 6, 2002
RadiationMonochromator: Double Crystal Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 20.5 Å2 / D resolution high: 1.45 Å / D resolution low: 34.14 Å / Number all: 49616 / Number obs: 48574 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.69 / Rsym value: 0.69 / NetI over sigmaI: 20.4 / Redundancy: 5 % / Percent possible obs: 97.8
Reflection shellRmerge I obs: 0.439 / Highest resolution: 1.45 Å / Lowest resolution: 1.5 Å / MeanI over sigI obs: 3.5 / Number unique all: 4310 / Rsym value: 0.439 / Redundancy: 5 % / Percent possible all: 88.4
Reflection shell
*PLUS
Number unique obs: 4310 / Percent possible obs: 88.4

+
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFC
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 50.2806 / Solvent model param ksol: 0.407671
Displacement parametersB iso mean: 27.8 Å2 / Aniso B11: -5.4 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 9.14 Å2 / Aniso B23: 0 Å2 / Aniso B33: -3.73 Å2
Least-squares processR factor R free: 0.224 / R factor R free error: 0.003 / R factor R work: 0.198 / R factor all: 0.201 / R factor obs: 0.201 / Highest resolution: 1.45 Å / Lowest resolution: 34.13 Å / Number reflection R free: 4783 / Number reflection all: 49616 / Number reflection obs: 48509 / Percent reflection R free: 9.9 / Percent reflection obs: 97.6
Refine analyzeLuzzati coordinate error free: 0.19 Å / Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.19 Å / Luzzati sigma a obs: 0.2 Å
Refine hist #LASTHighest resolution: 1.45 Å / Lowest resolution: 34.13 Å
Number of atoms included #LASTProtein: 2206 / Nucleic acid: 0 / Ligand: 3 / Solvent: 338 / Total: 2547
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.0
X-RAY DIFFRACTIONc_dihedral_angle_d14.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.011.50
X-RAY DIFFRACTIONc_mcangle_it2.712.00
X-RAY DIFFRACTIONc_scbond_it4.742.00
X-RAY DIFFRACTIONc_scangle_it7.252.50
Refine LS shellHighest resolution: 1.45 Å / R factor R free: 0.321 / R factor R free error: 0.012 / R factor R work: 0.306 / Lowest resolution: 1.54 Å / Number reflection R free: 699 / Number reflection R work: 6599 / Number reflection obs: 7298 / Total number of bins used: 6 / Percent reflection R free: 9.6 / Percent reflection obs: 89.6
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4MPD.PARAMMPD.TOP
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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