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- PDB-6l03: structure of PTP-MEG2 and MUNC18-1-pY145 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6l03
Titlestructure of PTP-MEG2 and MUNC18-1-pY145 peptide complex
Components
  • Tyrosine-protein phosphatase non-receptor type 9
  • stxbp1-pY145 peptide
KeywordsHYDROLASE / PTP-MEG2 / NSF / vesicle fusion
Function / homology
Function and homology information


positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / regulation of SNARE complex assembly / positive regulation of glutamate secretion, neurotransmission / regulation of synaptic vesicle fusion to presynaptic active zone membrane / developmental process involved in reproduction / axon target recognition / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / negative regulation of synaptic transmission, GABAergic ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / regulation of SNARE complex assembly / positive regulation of glutamate secretion, neurotransmission / regulation of synaptic vesicle fusion to presynaptic active zone membrane / developmental process involved in reproduction / axon target recognition / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / negative regulation of synaptic transmission, GABAergic / GABA synthesis, release, reuptake and degradation / regulation of synaptic vesicle priming / Acetylcholine Neurotransmitter Release Cycle / platelet degranulation / synaptic vesicle maturation / positive regulation of calcium ion-dependent exocytosis / Serotonin Neurotransmitter Release Cycle / presynaptic active zone cytoplasmic component / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / positive regulation of mast cell degranulation / Glutamate Neurotransmitter Release Cycle / neuromuscular synaptic transmission / platelet alpha granule / neurotransmitter secretion / neuron projection terminus / Interleukin-37 signaling / vesicle docking involved in exocytosis / syntaxin binding / syntaxin-1 binding / long-term synaptic depression / Neurexins and neuroligins / SNARE complex assembly / synaptic vesicle priming / parallel fiber to Purkinje cell synapse / phospholipase binding / peptidyl-tyrosine dephosphorylation / negative regulation of protein-containing complex assembly / presynaptic cytosol / protein dephosphorylation / vesicle-mediated transport / phagocytic vesicle / presynaptic active zone membrane / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / SNARE binding / secretory granule / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / Regulation of insulin secretion / cellular response to type II interferon / platelet aggregation / response to estradiol / negative regulation of neuron projection development / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / protein stabilization / protein domain specific binding / axon / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain ...Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 9 / Syntaxin-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.084 Å
AuthorsXu, Y.F. / Chen, X. / Yu, X. / Sun, J.P.
CitationJournal: Embo Rep. / Year: 2021
Title: PTP-MEG2 regulates quantal size and fusion pore opening through two distinct structural bases and substrates.
Authors: Xu, Y.F. / Chen, X. / Yang, Z. / Xiao, P. / Liu, C.H. / Li, K.S. / Yang, X.Z. / Wang, Y.J. / Zhu, Z.L. / Xu, Z.G. / Zhang, S. / Wang, C. / Song, Y.C. / Zhao, W.D. / Wang, C.H. / Ji, Z.L. / ...Authors: Xu, Y.F. / Chen, X. / Yang, Z. / Xiao, P. / Liu, C.H. / Li, K.S. / Yang, X.Z. / Wang, Y.J. / Zhu, Z.L. / Xu, Z.G. / Zhang, S. / Wang, C. / Song, Y.C. / Zhao, W.D. / Wang, C.H. / Ji, Z.L. / Zhang, Z.Y. / Cui, M. / Sun, J.P. / Yu, X.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 9
F: stxbp1-pY145 peptide


Theoretical massNumber of molelcules
Total (without water)36,3162
Polymers36,3162
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-9 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.048, 84.074, 48.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 9 / Protein-tyrosine phosphatase MEG2 / PTPase MEG2


Mass: 35208.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN9 / Production host: Escherichia coli (E. coli) / References: UniProt: P43378, protein-tyrosine-phosphatase
#2: Protein/peptide stxbp1-pY145 peptide


Mass: 1107.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61764*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000, 0.2M KSCN, 10% ethelene glycol, 0.1M bis-tris propane

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.08→54.3 Å / Num. obs: 18019 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 6.5
Reflection shellResolution: 2.08→2.2 Å / Rmerge(I) obs: 0.927 / Num. unique obs: 1773

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ICZ

4icz


Resolution: 2.084→54.266 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 896 4.98 %
Rwork0.2102 17099 -
obs0.2113 17995 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.9 Å2 / Biso mean: 35.7581 Å2 / Biso min: 18.19 Å2
Refinement stepCycle: final / Resolution: 2.084→54.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 0 79 2519
Biso mean---37.48 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082494
X-RAY DIFFRACTIONf_angle_d0.9683376
X-RAY DIFFRACTIONf_chiral_restr0.051367
X-RAY DIFFRACTIONf_plane_restr0.005434
X-RAY DIFFRACTIONf_dihedral_angle_d7.4042058
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.084-2.21450.36391330.29142813100
2.2145-2.38550.27651500.25762797100
2.3855-2.62560.28741380.24192845100
2.6256-3.00550.2671600.23572817100
3.0055-3.78650.19471520.19912846100
3.7865-54.2660.19481630.1749298199

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