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- PDB-1sfc: NEURONAL SYNAPTIC FUSION COMPLEX -

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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


trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / positive regulation of norepinephrine secretion / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / zymogen granule membrane / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulation of establishment of protein localization / presynaptic dense core vesicle exocytosis / ribbon synapse / storage vacuole / synaptic vesicle docking / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / vesicle docking / chloride channel inhibitor activity / Golgi to plasma membrane protein transport / SNARE complex / SNAP receptor activity / secretion by cell / regulation of vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / neurotransmitter secretion / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter receptor internalization / neuron projection terminus / neurotransmitter transport / ATP-dependent protein binding / protein localization to membrane / regulation of synaptic vesicle recycling / syntaxin-1 binding / insulin secretion / SNARE complex assembly / positive regulation of neurotransmitter secretion / synaptic vesicle priming / syntaxin binding / Neutrophil degranulation / clathrin-coated vesicle / regulation of synapse assembly / endosomal transport / myosin binding / modulation of excitatory postsynaptic potential / regulation of neuron projection development / exocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / voltage-gated potassium channel activity / positive regulation of excitatory postsynaptic potential / associative learning / protein sumoylation / synaptic vesicle endocytosis / long-term memory / endomembrane system / calcium channel inhibitor activity / response to glucose / voltage-gated potassium channel complex / axonal growth cone / presynaptic active zone membrane / vesicle-mediated transport / somatodendritic compartment / photoreceptor inner segment / axonogenesis / SNARE binding / acrosomal vesicle / locomotory behavior / filopodium / secretory granule / long-term synaptic potentiation / establishment of localization in cell / postsynaptic density membrane / phospholipid binding / intracellular protein transport
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Non-polymers , 3 types, 39 molecules

#5: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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