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- PDB-1hvv: SELF-ASSOCIATION OF THE H3 REGION OF SYNTAXIN 1A: IMPLICATIONS FO... -

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Basic information

Entry
Database: PDB / ID: 1hvv
TitleSELF-ASSOCIATION OF THE H3 REGION OF SYNTAXIN 1A: IMPLICATIONS FOR SNARE COMPLEX ASSEMBLY
ComponentsSYNTAXIN 1ASTX1A
KeywordsENDOCYTOSIS/EXOCYTOSIS / four-helix bundle / homotetramer / alpha-helix / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


myosin head/neck binding / Other interleukin signaling / 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 / positive regulation of norepinephrine secretion / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...myosin head/neck binding / Other interleukin signaling / 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 / positive regulation of norepinephrine secretion / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / 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 / synaptic vesicle docking / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of calcium ion-dependent exocytosis / vesicle docking / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / secretion by cell / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / regulation of exocytosis / ATP-dependent protein binding / neurotransmitter transport / protein localization to membrane / SNARE complex assembly / positive regulation of neurotransmitter secretion / insulin secretion / myosin binding / modulation of excitatory postsynaptic potential / exocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of excitatory postsynaptic potential / protein sumoylation / synaptic vesicle endocytosis / endomembrane system / calcium channel inhibitor activity / presynaptic active zone membrane / SNARE binding / acrosomal vesicle / secretory granule / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / kinase binding / calcium-dependent protein binding / protein-macromolecule adaptor activity / synaptic vesicle / presynapse / presynaptic membrane / nuclear membrane / transmembrane transporter binding / postsynaptic density / neuron projection / axon / synapse / glutamatergic synapse / protein-containing complex binding / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / 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
D(-)-TARTARIC ACID / Syntaxin-1A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.4 Å
AuthorsMisura, K.M.S. / Scheller, R.H. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Self-association of the H3 region of syntaxin 1A. Implications for intermediates in SNARE complex assembly.
Authors: Misura, K.M. / Scheller, R.H. / Weis, W.I.
History
DepositionJan 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SYNTAXIN 1A
B: SYNTAXIN 1A
C: SYNTAXIN 1A
D: SYNTAXIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5785
Polymers35,4284
Non-polymers1501
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-108 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.320, 88.320, 115.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is an anti-parallel homotetramer contained within one asymmetric unit.

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Components

#1: Protein
SYNTAXIN 1A / STX1A / NEURON-SPECIFIC ANTIGEN HPC-1 / SYNAPTOTAGMIN ASSOCIATED 35 KDA PROTEIN


Mass: 8857.096 Da / Num. of mol.: 4 / Fragment: RESIDUES 190-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: STX1A / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): AB1899 / References: UniProt: P32851
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.67 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium potassium tartrate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
2300 mM1dropNaCl
315 mMTris1drop
4750 mMsodium potassium tartrate1reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 3, 1995 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. all: 21053 / Num. obs: 20870 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.8
Reflection shellResolution: 2.4→45 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.313 / % possible all: 99.1
Reflection
*PLUS
Redundancy: 4.4 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 99.1 % / Redundancy: 3.8 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2243567.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1563 7.8 %RANDOM
Rwork0.238 ---
all0.238 20870 --
obs0.238 20125 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.2 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å27.68 Å20 Å2
2--1.6 Å20 Å2
3----3.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-6 Å
Luzzati sigma a0.26 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 10 53 2141
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_d15.7
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 2.4→2.47 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 244 7.8 %
Rwork0.244 2875 -
obs-1710 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TAR.PARAMTAR.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.7 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_deg15.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
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: 0.286 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.244

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