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- PDB-7xsj: The structure of the Mint1/Munc18-1/syntaxin-1 complex -

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Basic information

Entry
Database: PDB / ID: 7xsj
TitleThe structure of the Mint1/Munc18-1/syntaxin-1 complex
Components
  • Amyloid-beta A4 precursor protein-binding family A member 1
  • Syntaxin-1A
  • Syntaxin-binding protein 1
KeywordsPROTEIN BINDING / Munc18-1 / Mint1-MID / Syntaxin-1 / the Mint1-MID-Munc18-1-syntaxin-1 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 / negative regulation of synaptic transmission, GABAergic / myosin head/neck binding / Other interleukin signaling ...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 / negative regulation of synaptic transmission, GABAergic / myosin head/neck binding / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / gamma-aminobutyric acid secretion / platelet degranulation / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / synaptic vesicle maturation / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / regulation of synaptic vesicle priming / regulated exocytosis / presynaptic active zone cytoplasmic component / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of calcium ion-dependent exocytosis / positive regulation of mast cell degranulation / vesicle docking / regulation of exocytosis / secretion by cell / chloride channel inhibitor activity / platelet alpha granule / SNAP receptor activity / SNARE complex / calcium-ion regulated exocytosis / neuromuscular synaptic transmission / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / ATP-dependent protein binding / neurotransmitter secretion / vesicle docking involved in exocytosis / glutamate secretion / long-term synaptic depression / protein localization to membrane / syntaxin binding / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / synaptic vesicle priming / myosin binding / response to gravity / parallel fiber to Purkinje cell synapse / exocytosis / 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 / calcium channel inhibitor activity / phospholipase binding / presynaptic cytosol / phagocytic vesicle / presynaptic active zone membrane / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / endomembrane system / acrosomal vesicle / secretory granule / SNARE binding / protein localization to plasma membrane / PDZ domain binding / locomotory behavior / intracellular protein transport / establishment of localization in cell / postsynaptic density membrane / cellular response to type II interferon / platelet aggregation / kinase binding / Schaffer collateral - CA1 synapse / multicellular organism growth / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / response to estradiol / presynapse / amyloid-beta binding / presynaptic membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / 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 / Phosphotyrosine interaction domain (PTB/PID) / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / PDZ domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Amyloid-beta A4 precursor protein-binding family A member 1 / Syntaxin-1A / Syntaxin-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFeng, W. / Li, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071191 China
National Natural Science Foundation of China (NSFC)31971160 China
CitationJournal: Structure / Year: 2023
Title: A non-canonical target-binding site in Munc18-1 domain 3b for assembling the Mint1-Munc18-1-syntaxin-1 complex.
Authors: Li, W. / Xing, Y. / Wang, Y. / Xu, T. / Song, E. / Feng, W.
History
DepositionMay 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Amyloid-beta A4 precursor protein-binding family A member 1


Theoretical massNumber of molelcules
Total (without water)106,6143
Polymers106,6143
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-26 kcal/mol
Surface area36350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.238, 156.238, 78.857
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 / Munc18-1


Mass: 68240.289 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61765
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 28880.598 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P32851
#3: Protein Amyloid-beta A4 precursor protein-binding family A member 1 / Adapter protein X11alpha / Neuron-specific X11 protein / Neuronal Munc18-1-interacting protein 1 / Mint-1


Mass: 9493.023 Da / Num. of mol.: 1 / Fragment: MID
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Apba1, Mint1, X11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O35430

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium Malonate, pH 7.0, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 16652 / % possible obs: 100 % / Redundancy: 25.4 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.022 / Rrim(I) all: 0.111 / Χ2: 1.352 / Net I/σ(I): 9.2 / Num. measured all: 422820
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.310.83716300.9680.1670.8531.413100
3.31-3.450.57416320.9860.1140.5851.432100
3.45-3.60.40116180.9910.080.4091.415100
3.6-3.790.27616440.9960.0550.2811.475100
3.79-4.030.20616330.9980.0410.211.541100
4.03-4.340.14816550.9980.030.1511.628100
4.34-4.780.10916490.9990.0220.1121.5100
4.78-5.470.08816800.9990.0180.091.178100
5.47-6.890.07316990.9990.0150.0741.098100
6.89-500.043181210.0430.85299.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JEH

4jeh


Resolution: 3.2→41.87 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 824 4.96 %
Rwork0.235 15779 -
obs0.2367 16603 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.84 Å2 / Biso mean: 64.314 Å2 / Biso min: 18.67 Å2
Refinement stepCycle: final / Resolution: 3.2→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6400 0 0 0 6400
Num. residues----798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.40.38881270.329225792706100
3.4-3.660.32491390.293125652704100
3.66-4.030.3041230.261826032726100
4.03-4.610.24571550.23142597275299
4.62-5.810.30181330.232626422775100
5.81-41.870.22231470.19627932940100
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)
12.5798-0.40250.96342.4993-0.43761.1833-0.0515-0.469-0.47650.4175-0.00960.41470.0446-0.19870.04690.9461-0.00810.2140.86680.07911.0616-35.958-20.35216.378
22.96291.10621.23952.37390.96382.2314-0.21230.24140.2663-0.29820.01650.7968-0.51020.14330.23480.91040.0019-0.1220.88720.05071.1273-42.2282.595-4.1
31.5298-0.17070.46041.27390.88843.31910.0996-0.0986-0.6221-0.0535-0.05770.92930.0448-0.2413-0.01990.8522-0.02280.00240.8264-0.00991.7269-54.828-15.6340.282
45.7712-4.3586-2.2113.6152.33533.0201-1.1087-1.3776-0.15342.01661.0179-0.01150.32320.48690.20651.32560.00520.07521.107-0.00150.813-13.2372.86628.265
53.408-1.9311-0.52775.36811.66512.5992-0.1373-0.36610.3428-0.01990.0411-1.5636-0.53570.0066-0.14181.1806-0.1925-0.00521.0230.01640.9747-9.44510.46523.186
62.8073-2.1951-2.8684.46922.46952.99330.2641-0.2322-0.781.2357-0.248-0.70411.01790.0686-0.18081.3813-0.0174-0.23280.8474-0.0661.2695-4.407-18.1457.024
72.2077-1.5392-0.58612.75811.0531.0196-0.05340.0596-0.0371-0.29530.04690.7021-0.2803-0.32330.10491.1424-0.0188-0.00031.0045-0.010.8004-22.45318.97918.966
81.793-0.299-2.23420.05060.38272.87031.3652-0.2354-0.754-0.4066-0.02340.6095-0.9828-0.2469-0.89541.75330.0441-0.10711.1355-0.12932.0259-24.79446.67724.87
92.485-0.6687-0.2238.38352.49851.9376-0.2683-0.31480.19450.77270.387-0.47040.21080.1491-0.04081.502-0.11910.09761.09120.06490.8805-17.19222.55319.154
104.69136.1184-1.06159.21881.54188.15960.8843-0.05981.5416-0.41380.53681.5462-1.19040.3538-0.99031.3548-0.0825-0.070.8850.05281.0424-23.673-6.8859.375
117.4349-0.19933.02014.9021-6.4939.6207-0.6093-0.136-0.7250.06530.9840.66470.42140.66310.09631.1220.07140.24290.87650.23450.9438-23.803-14.2589.834
122.1733-3.48711.60277.2326-0.42594.3077-0.31470.3118-2.0202-0.14430.8840.13260.61160.5869-0.3341.60.29970.50111.36540.12231.7621-12.604-24.2087.795
131.30350.28170.2361.18-0.33860.2346-0.2887-0.3131-0.0011.39240.4534-0.5036-0.56210.2249-0.15252.1328-0.0116-0.42021.4906-0.35942.506-66.978-15.2-23.861
145.3811-2.8573-3.85095.3371-0.15384.02290.3992-0.2711-0.2833-0.20380.655-0.5911-0.8117-1.0187-0.39211.39530.3506-0.84592.0951-0.39742.1482-56.648-10.397-31.559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:280 )A4 - 280
2X-RAY DIFFRACTION2( CHAIN A AND RESID 281:416 )A281 - 416
3X-RAY DIFFRACTION3( CHAIN A AND RESID 417:594 )A417 - 594
4X-RAY DIFFRACTION4( CHAIN B AND RESID 29:62 )B29 - 62
5X-RAY DIFFRACTION5( CHAIN B AND RESID 63:105 )B63 - 105
6X-RAY DIFFRACTION6( CHAIN B AND RESID 106:110 )B106 - 110
7X-RAY DIFFRACTION7( CHAIN B AND RESID 111:176 )B111 - 176
8X-RAY DIFFRACTION8( CHAIN B AND RESID 177:185 )B177 - 185
9X-RAY DIFFRACTION9( CHAIN B AND RESID 186:226 )B186 - 226
10X-RAY DIFFRACTION10( CHAIN B AND RESID 227:232 )B227 - 232
11X-RAY DIFFRACTION11( CHAIN B AND RESID 233:237 )B233 - 237
12X-RAY DIFFRACTION12( CHAIN B AND RESID 238:247 )B238 - 247
13X-RAY DIFFRACTION13( CHAIN C AND RESID 266:270 )C266 - 270
14X-RAY DIFFRACTION14( CHAIN C AND RESID 271:283 )C271 - 283

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