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- PDB-6lpc: Crystal Structure of rat Munc18-1 with K332E/K333E mutation -

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Basic information

Entry
Database: PDB / ID: 6lpc
TitleCrystal Structure of rat Munc18-1 with K332E/K333E mutation
ComponentsSyntaxin-binding protein 1
KeywordsEXOCYTOSIS / Synaptic exocytosis / Membrane fusion / SNAREs-binding
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 / presynaptic dense core vesicle exocytosis / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...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 / presynaptic dense core vesicle exocytosis / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / negative regulation of synaptic transmission, GABAergic / regulation of synaptic vesicle priming / platelet degranulation / synaptic vesicle maturation / positive regulation of calcium ion-dependent exocytosis / presynaptic active zone cytoplasmic component / positive regulation of mast cell degranulation / neuromuscular synaptic transmission / platelet alpha granule / neurotransmitter secretion / vesicle docking involved in exocytosis / syntaxin binding / syntaxin-1 binding / long-term synaptic depression / SNARE complex assembly / synaptic vesicle priming / parallel fiber to Purkinje cell synapse / exocytosis / phospholipase binding / positive regulation of exocytosis / negative regulation of protein-containing complex assembly / presynaptic cytosol / phagocytic vesicle / SNARE binding / secretory granule / protein localization to plasma membrane / establishment of localization in cell / intracellular protein transport / terminal bouton / cellular response to type II interferon / platelet aggregation / response to estradiol / presynapse / neuron apoptotic process / molecular adaptor activity / negative regulation of neuron apoptotic process / postsynapse / protein stabilization / protein domain specific binding / axon / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / protein-containing complex / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Alpha-Beta Complex ...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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Syntaxin-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.402 Å
AuthorsWang, X.P. / Gong, J.H. / Wang, S. / Zhu, L. / Yang, X.Y. / Xu, Y.Y. / Yang, X.F. / Ma, C.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670846 China
National Basic Research Program of China (973 Program)2015CB910800 China
National Natural Science Foundation of China (NSFC)31721002 China
National Natural Science Foundation of China (NSFC)31670850 China
CitationJournal: Embo J. / Year: 2020
Title: Munc13 activates the Munc18-1/syntaxin-1 complex and enables Munc18-1 to prime SNARE assembly.
Authors: Wang, X. / Gong, J. / Zhu, L. / Wang, S. / Yang, X. / Xu, Y. / Yang, X. / Ma, C.
History
DepositionJan 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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-binding protein 1


Theoretical massNumber of molelcules
Total (without water)135,3312
Polymers135,3312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer, but displaying dimerization in crystal packing.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-26 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.475, 80.475, 247.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 6 or (resid 7...
21(chain B and (resid 1 through 61 or (resid 62...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU(chain A and (resid 1 through 6 or (resid 7...AA1 - 61 - 6
12LYSLYSALAALA(chain A and (resid 1 through 6 or (resid 7...AA7 - 87 - 8
13METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
14METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
15METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
16METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
21METMETILEILE(chain B and (resid 1 through 61 or (resid 62...BB1 - 611 - 61
22ASNASNGLUGLU(chain B and (resid 1 through 61 or (resid 62...BB62 - 6662 - 66
23METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585
24METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585
25METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585
26METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585

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Components

#1: Protein Syntaxin-binding protein 1 / Munc18-1 / N-Sec1 / Protein unc-18 homolog 1 / Unc18-1 / Protein unc-18 homolog A / Unc-18A / p67 / rbSec1


Mass: 67665.570 Da / Num. of mol.: 2 / Mutation: K332E, K333E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stxbp1, Unc18a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61765

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4 M ammonium acetate, 0.1 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 21586 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.033 / Rrim(I) all: 0.078 / Χ2: 1.029 / Net I/σ(I): 25.2
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2162 / CC1/2: 0.934 / CC star: 0.983 / Rpim(I) all: 0.281 / Rrim(I) all: 0.658 / Χ2: 0.66 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHASERphasing
SCALAdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PUJ

3puj


Resolution: 3.402→49.072 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.96
RfactorNum. reflection% reflection
Rfree0.3306 1102 5.14 %
Rwork0.2809 --
obs0.2834 21456 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 252.62 Å2 / Biso mean: 135.813 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.402→49.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7114 0 0 0 7114
Num. residues----1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057241
X-RAY DIFFRACTIONf_angle_d0.8349914
X-RAY DIFFRACTIONf_chiral_restr0.0471206
X-RAY DIFFRACTIONf_plane_restr0.0061289
X-RAY DIFFRACTIONf_dihedral_angle_d4.5224353
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3590X-RAY DIFFRACTION11.268TORSIONAL
12B3590X-RAY DIFFRACTION11.268TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.402-3.55680.43551610.3734251399
3.5568-3.74430.39591340.349251599
3.7443-3.97880.40521280.33532567100
3.9788-4.28580.34691360.30722534100
4.2858-4.71680.36511340.29922556100
4.7168-5.39860.33091490.29962541100
5.3986-6.79880.33661260.33052564100
6.7988-49.0720.27331340.2167256499

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