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- PDB-6kzq: structure of PTP-MEG2 and NSF-pY83 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6kzq
Titlestructure of PTP-MEG2 and NSF-pY83 peptide complex
Components
  • NSF-pY83 peptide
  • Tyrosine-protein phosphatase non-receptor type 9
KeywordsHYDROLASE / PTP-MEG2 / NSF / vesicle fusion
Function / homology
Function and homology information


: / Retrograde transport at the Trans-Golgi-Network / Trafficking of GluR2-containing AMPA receptors / Intra-Golgi traffic / SNARE complex disassembly / regulation of exocytosis / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack ...: / Retrograde transport at the Trans-Golgi-Network / Trafficking of GluR2-containing AMPA receptors / Intra-Golgi traffic / SNARE complex disassembly / regulation of exocytosis / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / Interleukin-37 signaling / COPII-mediated vesicle transport / syntaxin-1 binding / protein dephosphorylation / vesicle-fusing ATPase / COPI-dependent Golgi-to-ER retrograde traffic / neuron projection terminus / peptidyl-tyrosine dephosphorylation / exocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of receptor recycling / COPI-mediated anterograde transport / vesicle-mediated transport / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / ionotropic glutamate receptor binding / dendritic shaft / positive regulation of protein localization to plasma membrane / SNARE binding / PDZ domain binding / potassium ion transport / intracellular protein transport / positive regulation of protein catabolic process / negative regulation of neuron projection development / postsynaptic density / lysosomal membrane / protein kinase binding / protein-containing complex binding / Golgi apparatus / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / NSF, AAA+ ATPase lid domain / : / Vesicle-fusing ATPase / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / : / NSF, AAA+ ATPase lid domain / : / Vesicle-fusing ATPase / 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 / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 9 / Vesicle-fusing ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Nov 6, 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: NSF-pY83 peptide


Theoretical massNumber of molelcules
Total (without water)36,3912
Polymers36,3912
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-7 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.447, 83.708, 48.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

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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 NSF-pY83 peptide


Mass: 1182.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P46459*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 1.99 Å3/Da / Density % sol: 38.26 %
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32748 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.81 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.188 / Net I/σ(I): 8.1 / Num. measured all: 237798
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.7-1.767.20.54231670.678198.3
1.76-1.837.30.3932160.753199.4
1.83-1.917.30.29632150.87199.5
1.91-2.027.30.20232370.958199.7
2.02-2.147.30.15932371.16199.8
2.14-2.317.30.1332761.295199.8
2.31-2.547.30.10632681.418199.9
2.54-2.917.30.08832951.5221100
2.91-3.667.20.06333371.7921100
3.66-506.90.04535001.387199.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ICZ

4icz


Resolution: 1.7→36.233 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1662 5.08 %
Rwork0.1837 31050 -
obs0.185 32712 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.07 Å2 / Biso mean: 23.2073 Å2 / Biso min: 10.7 Å2
Refinement stepCycle: final / Resolution: 1.7→36.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 0 215 2622
Biso mean---31.78 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082438
X-RAY DIFFRACTIONf_angle_d1.0493300
X-RAY DIFFRACTIONf_chiral_restr0.049364
X-RAY DIFFRACTIONf_plane_restr0.006419
X-RAY DIFFRACTIONf_dihedral_angle_d6.6962511
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.74960.32241430.2597248898
1.7496-1.80610.2451460.21792540100
1.8061-1.87060.24721480.1961252199
1.8706-1.94550.22141420.18032563100
1.9455-2.0340.22111430.17572549100
2.034-2.14130.18491430.16832538100
2.1413-2.27540.20931170.17262606100
2.2754-2.45110.20931410.17692591100
2.4511-2.69760.2211290.18512605100
2.6976-3.08780.23791310.19062621100
3.0878-3.88960.17851400.16872641100
3.8896-36.2330.1951390.19042787100

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