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- PDB-3c98: Revised structure of the munc18a-syntaxin1 complex -

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Basic information

Entry
Database: PDB / ID: 3c98
TitleRevised structure of the munc18a-syntaxin1 complex
Components
  • Syntaxin-1A
  • Syntaxin-binding protein 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / protein complex / Alternative splicing / Cytoplasm / Membrane / Phosphoprotein / Protein transport / Transport / Coiled coil / 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 / MAD / Resolution: 2.601 Å
AuthorsHattendorf, D.A. / Misura, K.M. / Burkhardt, P. / Scheller, R.H. / Fasshauer, D. / Weis, W.I.
Citation
Journal: Embo J. / Year: 2008
Title: Munc18a controls SNARE assembly through its interaction with the syntaxin N-peptide
Authors: Burkhardt, P. / Hattendorf, D.A. / Weis, W.I. / Fasshauer, D.
#1: Journal: Nature / Year: 2000
Title: Three-dimensional structure of the neuronal-Sec1-syntaxin 1a complex
Authors: Misura, K.M. / Scheller, R.H. / Weis, W.I.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionMar 25, 2008ID: 1DN1
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)101,5232
Polymers101,5232
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-17.5 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.070, 158.070, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Syntaxin-binding protein 1 / munc18A / Unc-18 homolog / Unc-18A / Unc-18-1 / N- Sec1 / rbSec1 / p67


Mass: 69071.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / References: UniProt: P61765
#2: Protein Syntaxin-1A / syntaxin1 / Synaptotagmin-associated 35 kDa protein / P35A / Neuron- specific antigen HPC-1


Mass: 32451.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE9 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG400, Ammonium Acetate, Sodium Acetate, EDTA, 2-mercaptoethanol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9798
SYNCHROTRONSSRL BL9-220.9252, 0.9795, 0.9798
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 4, 1999
ADSC QUANTUM 42CCDJul 4, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.92521
30.97951
ReflectionResolution: 2.6→33.88 Å / Num. all: 32718 / Num. obs: 32178 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.409 / Num. unique all: 3091 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.601→33.88 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / Isotropic thermal model: isotropic / σ(F): 0.03 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2332 8.01 %RANDOM
Rwork0.203 26798 --
obs0.208 29130 90.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.889 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 216.89 Å2 / Biso mean: 74.012 Å2 / Biso min: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.111 Å2-0 Å2-0 Å2
2---0.111 Å2-0 Å2
3---0.222 Å2
Refinement stepCycle: LAST / Resolution: 2.601→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6327 0 0 69 6396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036422
X-RAY DIFFRACTIONf_angle_d0.6698642
X-RAY DIFFRACTIONf_chiral_restr0.047983
X-RAY DIFFRACTIONf_plane_restr0.0021109
X-RAY DIFFRACTIONf_dihedral_angle_d14.9642492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.6540.319910.2961262135372.47
2.654-2.7120.3971270.3051387151481.53
2.712-2.7750.3571350.2881422155783.26
2.775-2.8450.3831520.2971419157184.46
2.845-2.9210.3531210.2781503162486.29
2.921-3.0070.3341200.2781520164088.08
3.007-3.1040.3141410.2651541168289.66
3.104-3.2150.3061340.2561601173592.93
3.215-3.3440.3351420.2441570171291.5
3.344-3.4960.2821490.241605175492.71
3.496-3.680.2851430.2171524166788.48
3.68-3.910.2871320.2041638177093.35
3.91-4.2120.2281340.1791668180294.44
4.212-4.6340.1971330.1421725185897.48
4.634-5.3030.2131580.1511752191099.07
5.303-6.6730.2541600.1871777193798.93
6.673-33.8840.1781600.1571884204498.41
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)
13.212-0.64620.12183.1179-0.9311.7027-0.145-0.4806-0.3920.55860.07870.14590.07850.14460.00010.7065-0.00750.12870.55980.03680.412253.917555.245222.9154
23.39810.2154-0.09492.2196-0.86933.3697-0.0604-0.4263-0.37980.50210.01960.67270.2212-0.0250.00010.5428-0.01490.15910.43240.06330.72529.735759.098412.9113
33.33160.98520.58322.09060.52952.0055-0.0780.16630.2212-0.2607-0.01970.5789-0.3378-0.0691-00.55870.0801-0.00660.3873-0.00320.670930.987273.702-3.122
40.05030.05610.0282-0.01250.0380.06210.0227-0.08790.59670.53360.301-0.119-0.1368-0.1522-0.00041.38990.00090.50791.82090.12720.995348.591846.756836.158
51.2253-0.1106-0.08624.21731.0181.75660.0433-0.12470.3663-0.01990.0514-0.0425-0.4980.0926-00.8155-0.19090.05880.7406-0.0290.475862.377490.997820.6303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 4-136A4 - 136
2X-RAY DIFFRACTION2chain A and (resid 137-235 or resid 532-592)A137 - 235
3X-RAY DIFFRACTION2chain A and (resid 137-235 or resid 532-592)A532 - 592
4X-RAY DIFFRACTION3chain A and resid 236-505A236 - 505
5X-RAY DIFFRACTION4chain B and resid 2-9B2 - 9
6X-RAY DIFFRACTION5chain B and resid 27-248B27 - 248

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