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- PDB-1ez3: CRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A -

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Basic information

Entry
Database: PDB / ID: 1ez3
TitleCRYSTAL STRUCTURE OF THE NEURONAL T-SNARE SYNTAXIN-1A
ComponentsSYNTAXIN-1A
KeywordsENDOCYTOSIS/EXOCYTOSIS / THREE HELIX BUNDLE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
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 / kinase binding / Schaffer collateral - CA1 synapse / 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLerman, J.C. / Robblee, J. / Fairman, R. / Hughson, F.M.
CitationJournal: Biochemistry / Year: 2000
Title: Structural analysis of the neuronal SNARE protein syntaxin-1A.
Authors: Lerman, J.C. / Robblee, J. / Fairman, R. / Hughson, F.M.
History
DepositionMay 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: SYNTAXIN-1A
B: SYNTAXIN-1A
C: SYNTAXIN-1A


Theoretical massNumber of molelcules
Total (without water)44,9363
Polymers44,9363
Non-polymers00
Water7,602422
1
A: SYNTAXIN-1A


Theoretical massNumber of molelcules
Total (without water)14,9791
Polymers14,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SYNTAXIN-1A


Theoretical massNumber of molelcules
Total (without water)14,9791
Polymers14,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SYNTAXIN-1A


Theoretical massNumber of molelcules
Total (without water)14,9791
Polymers14,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.410, 99.560, 54.960
Angle α, β, γ (deg.)90.00, 97.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SYNTAXIN-1A / SYNAPTOTAGMIN ASSOCIATED 35 KDA PROTEIN / P35A / NEURON-SPECIFIC ANTIGEN HPC-1


Mass: 14978.813 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PLM1 T7 PROMOTER PLASMID / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 1500, sodium acetate, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
210 mMdithiothreitol1drop
316 %PEG15001reservoir
420 mMsodium acetate1reservoirpH5.0
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98
DetectorType: OTHER / Detector: CCD / Date: Feb 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→28.748 Å / Num. all: 48323 / Num. obs: 48323 / % possible obs: 97.4 % / Redundancy: 4.53 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 37.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.423 / Num. unique all: 3862 / % possible all: 78.2
Reflection
*PLUS
Num. measured all: 155471

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1185796.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Used maximum likelihood using amplitudes and phase probability distribution.
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1456 5 %RANDOM
Rwork0.2305 ---
obs0.233 29081 99.1 %-
all-29272 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.64 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1-11.62 Å20 Å2-5.27 Å2
2---4.76 Å20 Å2
3----6.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 0 422 3492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d16
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 236 4.9 %
Rwork0.295 4602 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.359 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.295

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