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- PDB-4jeu: Crystal Structure of Munc18a and Syntaxin1 with native N-terminus... -

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Basic information

Entry
Database: PDB / ID: 4jeu
TitleCrystal Structure of Munc18a and Syntaxin1 with native N-terminus complex
Components
  • Syntaxin-1A
  • Syntaxin-binding protein 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / PROTEIN COMPLEX / MEMBRANE / PHOSPHOPROTEIN / PROTEIN TRANSPORT / TRANSPORT / NEUROTRANSMITTER TRANSPORT / TRANSMEMBRANE / ENDOCYTOSIS-EXOCYTOSIS complex
Function / homology
Function and homology information


positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / developmental process involved in reproduction / axon target recognition / regulation of vesicle fusion / myosin head/neck binding / Other interleukin signaling / presynaptic dense core vesicle exocytosis ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / developmental process involved in reproduction / axon target recognition / regulation of vesicle fusion / myosin head/neck binding / Other interleukin signaling / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II 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 / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / synaptic vesicle docking / negative regulation of synaptic transmission, GABAergic / regulation of synaptic vesicle priming / platelet degranulation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to gravity / synaptic vesicle maturation / positive regulation of calcium ion-dependent exocytosis / vesicle docking / presynaptic active zone cytoplasmic component / regulation of exocytosis / secretion by cell / SNAP receptor activity / SNARE complex / chloride channel inhibitor activity / vesicle fusion / positive regulation of mast cell degranulation / calcium-ion regulated exocytosis / LGI-ADAM interactions / actomyosin / hormone secretion / neuromuscular synaptic transmission / platelet alpha granule / neurotransmitter secretion / ATP-dependent protein binding / vesicle docking involved in exocytosis / protein localization to membrane / syntaxin binding / syntaxin-1 binding / long-term synaptic depression / insulin secretion / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / synaptic vesicle priming / myosin binding / parallel fiber to Purkinje cell synapse / exocytosis / phospholipase binding / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis / protein sumoylation / synaptic vesicle endocytosis / positive regulation of excitatory postsynaptic potential / negative regulation of protein-containing complex assembly / presynaptic cytosol / calcium channel inhibitor activity / phagocytic vesicle / presynaptic active zone membrane / endomembrane system / SNARE binding / acrosomal vesicle / secretory granule / protein localization to plasma membrane / establishment of localization in cell / intracellular protein transport / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cellular response to type II interferon / kinase binding / platelet aggregation / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / response to estradiol / presynapse / presynaptic membrane / protein-macromolecule adaptor activity / neuron apoptotic process / molecular adaptor activity / nuclear membrane / negative regulation of neuron apoptotic process / transmembrane transporter binding / postsynapse / neuron projection
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Syntaxin-1A / Syntaxin-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsColbert, K.N. / Hattendorf, D.A. / Weiss, T.M. / Burkhardt, P. / Fasshauer, D. / Weis, W.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Syntaxin1a variants lacking an N-peptide or bearing the LE mutation bind to Munc18a in a closed conformation.
Authors: Colbert, K.N. / Hattendorf, D.A. / Weiss, T.M. / Burkhardt, P. / Fasshauer, D. / Weis, W.I.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-binding protein 1
B: Syntaxin-1A


Theoretical massNumber of molelcules
Total (without water)95,3922
Polymers95,3922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-18 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.775, 156.775, 78.752
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Syntaxin-binding protein 1 / N-Sec1 / Protein unc-18 homolog 1 / Unc18-1 / Protein unc-18 homolog A / Unc-18A / p67 / rbSec1


Mass: 67289.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stxbp1, Unc18a / Production host: Escherichia coli (E. coli) / References: UniProt: P61765
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 28102.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jul 10, 2009
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.2→111.111 Å / Num. all: 16764 / Num. obs: 16764 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2-3.377.30.6771.11749423950.677100
3.37-3.587.30.3921.91648122710.392100
3.58-3.827.30.2423.11547821340.242100
3.82-4.137.30.1594.61451919990.159100
4.13-4.537.20.0997.51325618410.099100
4.53-5.067.10.0759.61208716930.075100
5.06-5.847.10.0848.61067314990.084100
5.84-7.1670.0729.8903412940.072100
7.16-10.126.70.03814.2688010200.038100
10.12-111.1116.10.03515.437756180.03599.8

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
X-PLORphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3C98

3c98


Resolution: 3.2→110.86 Å / Cor.coef. Fo:Fc: 0.9186 / Cor.coef. Fo:Fc free: 0.8799 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 1342 8.02 %RANDOM
Rwork0.199 ---
all0.318 16741 --
obs0.2042 16741 --
Displacement parametersBiso max: 255.58 Å2 / Biso mean: 97.9108 Å2 / Biso min: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.8188 Å20 Å20 Å2
2--10.8188 Å20 Å2
3----21.6377 Å2
Refine analyzeLuzzati coordinate error obs: 0.689 Å
Refinement stepCycle: LAST / Resolution: 3.2→110.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 0 0 6303
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3150SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes185HARMONIC2
X-RAY DIFFRACTIONt_gen_planes891HARMONIC5
X-RAY DIFFRACTIONt_it6399HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion864SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6399HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8611HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion3.54
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3212 260 8.75 %
Rwork0.2388 2713 -
all0.2459 2973 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.97270.05350.32840.48670.13070.35620.09630.04250.1010.3335-0.04020.6593-0.07460.1175-0.05610.1044-0.08070.1968-0.1353-0.03120.095435.633764.57527.8437
20.43540.2163-0.26050.94640.74200.1884-0.09030.17280.0085-0.12730.15620.11530.134-0.0610.3489-0.2510.1450.0624-0.1023-0.302161.229389.191320.8081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 592
2X-RAY DIFFRACTION2{ B|* }B2 - 243

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