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Basic information

Entry
Database: PDB / ID: 1jth
TitleCrystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a
Components
  • SNAP25
  • syntaxin 1a
KeywordsENDOCYTOSIS/EXOCYTOSIS / coiled-coil / polar layer / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


BLOC-1 complex / short-term synaptic potentiation / myosin head/neck binding / positive regulation of voltage-gated calcium channel activity / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / synaptic vesicle fusion to presynaptic active zone membrane ...BLOC-1 complex / short-term synaptic potentiation / myosin head/neck binding / positive regulation of voltage-gated calcium channel activity / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / 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 catecholamine secretion / regulation of establishment of protein localization / positive regulation of norepinephrine secretion / Dopamine Neurotransmitter Release Cycle / hormone secretion / regulation of synaptic vesicle priming / : / regulated exocytosis / secretion by cell / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of glutamate secretion, neurotransmission / calcium-ion regulated exocytosis / SNARE complex disassembly / positive regulation of calcium ion-dependent exocytosis / positive regulation of hormone secretion / positive regulation of neurotransmitter secretion / ribbon synapse / : / positive regulation of vesicle fusion / chloride channel inhibitor activity / regulation of exocytosis / protein carrier activity / SNARE complex / SNAP receptor activity / vesicle fusion / actomyosin / LGI-ADAM interactions / positive regulation of synaptic plasticity / neurotransmitter secretion / ATP-dependent protein binding / cytoplasmic side of membrane / insulin secretion / clathrin-dependent endocytosis / regulation of synaptic vesicle cycle / protein localization to membrane / syntaxin-1 binding / Neutrophil degranulation / regulation of neuron projection development / endosomal transport / exocytosis / regulation of synapse assembly / myosin binding / SNARE complex assembly / synaptic vesicle priming / response to gravity / synaptic vesicle exocytosis / neurotransmitter transport / positive regulation of exocytosis / associative learning / regulation of dopamine secretion / modulation of excitatory postsynaptic potential / protein sumoylation / axonal growth cone / voltage-gated potassium channel activity / synaptic vesicle endocytosis / long-term memory / calcium channel inhibitor activity / axonogenesis / photoreceptor inner segment / somatodendritic compartment / voltage-gated potassium channel complex / presynaptic active zone membrane / secretory granule / acrosomal vesicle / locomotory behavior / positive regulation of excitatory postsynaptic potential / SNARE binding / positive regulation of insulin secretion / filopodium / trans-Golgi network / intracellular protein transport / long-term synaptic potentiation / postsynaptic density membrane / Schaffer collateral - CA1 synapse / kinase binding / calcium-dependent protein binding / actin cytoskeleton / terminal bouton / synaptic vesicle membrane / neuron differentiation / synaptic vesicle / lamellipodium / nuclear membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / SNARE domain / 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
Syntaxin-1A / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMisura, K.M.S. / Gonzalez Jr., L.C. / May, A.P. / Scheller, R.H. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure and biophysical properties of a complex between the N-terminal SNARE region of SNAP25 and syntaxin 1a.
Authors: Misura, K.M. / Gonzalez Jr., L.C. / May, A.P. / Scheller, R.H. / Weis, W.I.
History
DepositionAug 21, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 16, 2014Group: Other
Revision 1.5Oct 23, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SNAP25
B: syntaxin 1a
C: SNAP25
D: syntaxin 1a


Theoretical massNumber of molelcules
Total (without water)37,2564
Polymers37,2564
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-109 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 65.780, 80.100
Angle α, β, γ (deg.)90.00, 99.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-93-

HOH

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Components

#1: Protein SNAP25 / synaptosomal-associated protein SNAP-25


Mass: 9525.569 Da / Num. of mol.: 2 / Fragment: N-terminal SNARE motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60881
#2: Protein syntaxin 1a


Mass: 9102.500 Da / Num. of mol.: 2 / Fragment: H3, SNARE motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): JM190 / References: UniProt: P32851
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails (eV)
115 mg/mlprotein1drop
2150 mM1dropNaCl
35 mMbeta-mercaptoethanol1drop
425 mMTris1droppH8.0
51.6 Mammonium sulfate1reservoir
6100 mMMES1reservoirpH6.5
710 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9292, 0.9795, 0.9797, 1.005
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 11, 2001 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92921
20.97951
30.97971
41.0051
ReflectionResolution: 2→30 Å / Num. all: 20657 / Num. obs: 18147 / % possible obs: 87.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.02 / Net I/σ(I): 24
Reflection shellResolution: 2→30 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8
Reflection
*PLUS
% possible obs: 96.8 % / Redundancy: 2.4 %
Reflection shell
*PLUS
% possible obs: 98.8 % / Redundancy: 2.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 549679.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2206 12.2 %RANDOM
Rwork0.266 ---
all-20657 --
obs-18147 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.652 Å2 / ksol: 0.37228 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å2-7.12 Å2
2--17.26 Å20 Å2
3----15.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 0 52 2057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d14.9
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.242.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 304 12.8 %
Rwork0.355 2080 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 12.2 % / Rfactor obs: 0.265 / Rfactor Rfree: 0.284
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scangle_it4.242.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / % reflection Rfree: 12.8 % / Rfactor Rwork: 0.355

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