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- PDB-4jeh: Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex -

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Basic information

Entry
Database: PDB / ID: 4jeh
TitleCrystal Structure of Munc18a and Syntaxin1 lacking N-peptide 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 / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / myosin head/neck binding / Other interleukin signaling / extrinsic component of presynaptic membrane ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / myosin head/neck binding / Other interleukin signaling / extrinsic component of presynaptic 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 / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / presynaptic dense core vesicle exocytosis / negative regulation of synaptic transmission, GABAergic / synaptic vesicle docking / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / neuromuscular synaptic transmission / platelet degranulation / synaptic vesicle maturation / vesicle docking / positive regulation of calcium ion-dependent exocytosis / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / presynaptic active zone cytoplasmic component / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of mast cell degranulation / platelet alpha granule / regulation of exocytosis / neurotransmitter secretion / protein localization to membrane / ATP-dependent protein binding / presynaptic cytosol / vesicle docking involved in exocytosis / neurotransmitter transport / parallel fiber to Purkinje cell synapse / insulin secretion / long-term synaptic depression / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / myosin binding / exocytosis / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / phospholipase binding / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / negative regulation of protein-containing complex assembly / presynaptic active zone membrane / vesicle-mediated transport / phagocytic vesicle / SNARE binding / acrosomal vesicle / secretory granule / establishment of localization in cell / protein localization to plasma membrane / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / kinase binding / platelet aggregation / cellular response to type II interferon / calcium-dependent protein binding / synaptic vesicle / presynapse / response to estradiol / protein-macromolecule adaptor activity / presynaptic membrane / postsynapse / nuclear membrane / neuron apoptotic process / transmembrane transporter binding / negative regulation of neuron apoptotic process / molecular adaptor activity
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, domain 2 / Sec1-like, domain 3a / Sec1-like protein ...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, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / 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 / 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: 2.5 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Syntaxin-binding protein 1
B: Syntaxin-1A


Theoretical massNumber of molelcules
Total (without water)97,5912
Polymers97,5912
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-15 kcal/mol
Surface area35460 Å2
MethodPISA
2
A: Syntaxin-binding protein 1
B: Syntaxin-1A

A: Syntaxin-binding protein 1
B: Syntaxin-1A


Theoretical massNumber of molelcules
Total (without water)195,1834
Polymers195,1834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area13170 Å2
ΔGint-34 kcal/mol
Surface area66290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.906, 154.906, 150.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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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: 69285.445 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: 28306.016 Da / Num. of mol.: 1 / Fragment: unp residues 24-266
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→62.017 Å / Num. all: 31771 / Num. obs: 31771 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.644.60.6461.12120945780.646100
2.64-2.84.60.471.52003943330.47100
2.8-2.994.60.2952.41893941000.295100
2.99-3.234.60.193.81752338240.19100
3.23-3.544.60.1175.71602635140.117100
3.54-3.954.50.0817.81439031910.08199.9
3.95-4.564.40.0688.91264628460.06899.7
4.56-5.594.20.05510.41002024010.05599.7
5.59-7.914.50.04215.2846818930.04299.3
7.91-62.8694.40.03415.7475310910.03498.3

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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
PHENIXphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3C98

3c98


Resolution: 2.5→32.64 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9258 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1996 6.29 %RANDOM
Rwork0.1843 ---
all0.255 31767 --
obs0.1867 31750 --
Displacement parametersBiso max: 157.16 Å2 / Biso mean: 59.4991 Å2 / Biso min: 26.57 Å2
Baniso -1Baniso -2Baniso -3
1-5.9181 Å20 Å20 Å2
2--5.9181 Å20 Å2
3----11.8361 Å2
Refine analyzeLuzzati coordinate error obs: 0.344 Å
Refinement stepCycle: LAST / Resolution: 2.5→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 0 69 6317
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013121SINUSOIDAL2
X-RAY DIFFRACTIONt_angle_deg1.1182HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.75885HARMONIC5
X-RAY DIFFRACTIONt_other_torsion3.196344HARMONIC20
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2427 182 6.32 %
Rwork0.2175 2700 -
all0.2191 2882 -
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)
11.17560.07340.11461.27480.67990.95480.0501-0.1935-0.45480.11470.04870.00730.135-0.0286-0.0988-0.1865-0.0031-0.0162-0.17420.130.013313.724434.840745.0106
23.48150.1122-0.790.4556-0.03160.50820.05410.14720.0294-0.0536-0.02840.08110.0235-0.1644-0.0257-0.0791-0.00150.0060.02080.0171-0.1208-11.887460.98557.9112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 592
2X-RAY DIFFRACTION2{ B|* }B27 - 247

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