[English] 日本語
Yorodumi
- PDB-1sfc: NEURONAL SYNAPTIC FUSION COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sfc
TitleNEURONAL SYNAPTIC FUSION COMPLEX
Components
  • (PROTEIN (SNAP- ...) x 2
  • PROTEIN (SYNAPTOBREVIN 2)
  • PROTEIN (SYNTAXIN 1A)
KeywordsTRANSPORT PROTEIN / MEMBRANE FUSION PROTEIN COMPLEX
Function / homology
Function and homology information


exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / BLOC-1 complex / Lysosome Vesicle Biogenesis / myosin head/neck binding / zymogen granule membrane / storage vacuole / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling ...exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / BLOC-1 complex / Lysosome Vesicle Biogenesis / myosin head/neck binding / 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 / Norepinephrine Neurotransmitter Release Cycle / 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 / positive regulation of calcium ion-dependent exocytosis / ribbon synapse / regulation of vesicle-mediated transport / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / secretion by cell / chloride channel inhibitor activity / Clathrin-mediated endocytosis / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / positive regulation of hormone secretion / neuron projection terminus / Golgi to plasma membrane protein transport / ATP-dependent protein binding / neurotransmitter secretion / protein localization to membrane / clathrin-coated vesicle / syntaxin binding / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / endosomal transport / Neutrophil degranulation / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / regulation of synapse assembly / myosin binding / synaptic vesicle priming / response to gravity / regulation of neuron projection development / exocytosis / associative learning / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis / protein sumoylation / synaptic vesicle endocytosis / voltage-gated potassium channel activity / positive regulation of excitatory postsynaptic potential / long-term memory / response to glucose / postsynaptic cytosol / axonal growth cone / calcium channel inhibitor activity / vesicle-mediated transport / presynaptic active zone membrane / somatodendritic compartment / voltage-gated potassium channel complex / photoreceptor inner segment / endomembrane system / acrosomal vesicle / axonogenesis / cytoplasmic vesicle membrane / secretory granule / SNARE binding / filopodium / locomotory behavior / intracellular protein transport / establishment of localization in cell / trans-Golgi network
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / 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. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
STRONTIUM ION / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsSutton, R.B. / Brunger, A.T.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 A resolution.
Authors: Sutton, R.B. / Fasshauer, D. / Jahn, R. / Brunger, A.T.
History
DepositionAug 24, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2013Group: Derived calculations
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_symmetry / _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.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.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (SYNAPTOBREVIN 2)
B: PROTEIN (SYNTAXIN 1A)
C: PROTEIN (SNAP-25B)
D: PROTEIN (SNAP-25B)
E: PROTEIN (SYNAPTOBREVIN 2)
F: PROTEIN (SYNTAXIN 1A)
G: PROTEIN (SNAP-25B)
H: PROTEIN (SNAP-25B)
I: PROTEIN (SYNAPTOBREVIN 2)
J: PROTEIN (SYNTAXIN 1A)
K: PROTEIN (SNAP-25B)
L: PROTEIN (SNAP-25B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,94532
Polymers118,97912
Non-polymers1,96620
Water34219
1
A: PROTEIN (SYNAPTOBREVIN 2)
B: PROTEIN (SYNTAXIN 1A)
C: PROTEIN (SNAP-25B)
D: PROTEIN (SNAP-25B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,42212
Polymers39,6604
Non-polymers7628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-107 kcal/mol
Surface area15000 Å2
MethodPISA
2
E: PROTEIN (SYNAPTOBREVIN 2)
F: PROTEIN (SYNTAXIN 1A)
G: PROTEIN (SNAP-25B)
H: PROTEIN (SNAP-25B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,33411
Polymers39,6604
Non-polymers6747
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-109 kcal/mol
Surface area14560 Å2
MethodPISA
3
I: PROTEIN (SYNAPTOBREVIN 2)
J: PROTEIN (SYNTAXIN 1A)
K: PROTEIN (SNAP-25B)
L: PROTEIN (SNAP-25B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1899
Polymers39,6604
Non-polymers5305
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-107 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.715, 111.071, 198.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 2 types, 6 molecules AEIBFJ

#1: Protein PROTEIN (SYNAPTOBREVIN 2) / VAMP 2


Mass: 10530.938 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P63045
#2: Protein PROTEIN (SYNTAXIN 1A)


Mass: 9603.944 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P32851

-
PROTEIN (SNAP- ... , 2 types, 6 molecules CGKDHL

#3: Protein PROTEIN (SNAP-25B)


Mass: 9662.756 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT
Source method: isolated from a genetically manipulated source
Details: ISOFORM SNAP-25'B' / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P60881
#4: Protein PROTEIN (SNAP-25B)


Mass: 9861.957 Da / Num. of mol.: 3 / Fragment: PROTEOLYTICALLY PROTECTED FRAGMENT
Source method: isolated from a genetically manipulated source
Details: ISOFORM SNAP-25'B' / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: NEURON / Plasmid: PET28-A / Production host: Escherichia coli (E. coli) / References: UniProt: P60881

-
Non-polymers , 3 types, 39 molecules

#5: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Sr
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 54.8 %
Crystal growpH: 7
Details: 35% MPD, 5% PEG350(MME), 25MM TRIS PH 7.0,. 70MM SRCL2, 250MM UREA, 7MM SARKOSYL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 29 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 %(v/v)MPD1reservoir
25 %(v/v)PEG350 MME1reservoir
325 mMTris-HCl1reservoir
470 mM1reservoirSrCl2
5250 mMurea1reservoir
624.5 %(v/v)MPD1drop
73.5 %(v/v)PEG350 MME1drop
817.5 mMTris1drop
949 mM1dropSrCl2
10175 mMurea1drop
113.75 mMSarkosyl1drop
1210 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0332,0.9797,1.0688,0.9801,0.9795,0.9800
DetectorType: ADSC / Detector: CCD / Date: May 15, 1998 / Details: BENT MIRROR
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.97971
31.06881
40.98011
50.97951
60.981
ReflectionResolution: 2.4→50 Å / Num. obs: 42980 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 10 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 7.6 / Rsym value: 0.309 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 309408 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.329

-
Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
DENZOdata reduction
d*TREKdata scaling
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 5215518.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.303 7990 9.8 %RANDOM
Rwork0.265 ---
obs0.265 81606 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.46 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--8.86 Å20 Å2
3----10.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7017 0 69 19 7105
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it4.212.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 1338 9.9 %
Rwork0.337 12128 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PAR_SR.PROTOPSR.PRO
X-RAY DIFFRACTION3MPD.PARMPD.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.337

+
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