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- PDB-5ez0: CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE PDZ ... -

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Basic information

Entry
Database: PDB / ID: 5ez0
TitleCRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE PDZ BINDING MOTIF OF THE MITOGEN ACTIVATED PROTEIN KINASE P38GAMMA.
Components
  • Mitogen-activated protein kinase 12P38 mitogen-activated protein kinases
  • Tyrosine-protein phosphatase non-receptor type 4
KeywordsAPOPTOSIS / CELL DEATH / GLIOBLASTOMA / MULTIPROTEIN COMPLEXES / PDZ DOMAINS / P38GAMMA / MITOGEN ACTIVATED PROTEIN KINASE / PROTEIN BINDING / NON-RECEPTOR TYPE 4 / PTPN4 / RABIES VIRUS / PDZ BINDING MOTIF
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / MAP kinase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / MAP kinase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / cytoskeleton / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain ...Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / Mitogen-activated protein (MAP) kinase p38-like / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PDZ domain / Pdz3 Domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase 12 / Tyrosine-protein phosphatase non-receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMaisonneuve, P. / Vaney, M.C. / Caillet-Saguy, C. / Lafon, M. / Delepierre, M. / Cordier, F. / Wolff, N.
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38 gamma.
Authors: Maisonneuve, P. / Caillet-Saguy, C. / Vaney, M.C. / Bibi-Zainab, E. / Sawyer, K. / Raynal, B. / Haouz, A. / Delepierre, M. / Lafon, M. / Cordier, F. / Wolff, N.
#1: Journal: Structure / Year: 2011
Title: Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death.
Authors: Babault, N. / Cordier, F. / Lafage, M. / Cockburn, J. / Haouz, A. / Prehaud, C. / Rey, F.A. / Delepierre, M. / Buc, H. / Lafon, M. / Wolff, N.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Dec 20, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 4
B: Tyrosine-protein phosphatase non-receptor type 4
C: Tyrosine-protein phosphatase non-receptor type 4
D: Tyrosine-protein phosphatase non-receptor type 4
E: Mitogen-activated protein kinase 12
F: Mitogen-activated protein kinase 12
G: Mitogen-activated protein kinase 12
H: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,07110
Polymers51,8798
Non-polymers1922
Water1,71195
1
A: Tyrosine-protein phosphatase non-receptor type 4
E: Mitogen-activated protein kinase 12


Theoretical massNumber of molelcules
Total (without water)12,9702
Polymers12,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 4
F: Mitogen-activated protein kinase 12


Theoretical massNumber of molelcules
Total (without water)12,9702
Polymers12,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase non-receptor type 4
G: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0663
Polymers12,9702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein phosphatase non-receptor type 4
H: Mitogen-activated protein kinase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0663
Polymers12,9702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.564, 76.121, 198.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1046, -0.9945, 0.002796), (-0.9945, 0.1046, -0.002913), (0.002604, -0.003086, -1)-3.045, -36.970001, 49.5
2given(-0.3802, 0.7502, 0.541), (0.7591, -0.08106, 0.6459), (0.5284, 0.6562, -0.5387)-19.02, -27.9, 46.720001
3given(-0.7131, 0.4478, -0.5395), (0.001061, -0.7688, -0.6395), (-0.7011, -0.4566, 0.5477)22.42, -24.58, 0.8664

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Components

#1: Protein
Tyrosine-protein phosphatase non-receptor type 4 / Protein-tyrosine phosphatase MEG1 / PTPase-MEG1


Mass: 11694.363 Da / Num. of mol.: 4 / Fragment: PDZ DOMAIN, RESIDUES 499-604
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN4 / Plasmid: PDEST15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29074, protein-tyrosine-phosphatase
#2: Protein/peptide
Mitogen-activated protein kinase 12 / P38 mitogen-activated protein kinases / Mitogen-activated protein kinase 12 / isoform CRA_a


Mass: 1275.453 Da / Num. of mol.: 4 / Fragment: PDZ BINDING MOTIF, RESIDUES 269-277 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B5MDL5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.2 M SODIUM DI-HYDROGEN PHOSPHATE 0.8 M DI-POTASSIUM HYDROGEN PHOSPHATE 0.1M CAPS 0.2 M Lithium sulfate 0.67 M Non-Detergent Sulfobetaine (NDSB) 201

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2011
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.35→49.35 Å / Num. obs: 21504 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 49.27 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / Rejects: 0 / % possible all: 93.7

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.4refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NFK

3nfk


Resolution: 2.35→45.33 Å / Cor.coef. Fo:Fc: 0.9124 / Cor.coef. Fo:Fc free: 0.8969 / SU R Cruickshank DPI: 0.329 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.23
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 1088 5.07 %RANDOM
Rwork0.2284 ---
obs0.2295 21464 97.07 %-
Displacement parametersBiso max: 106.09 Å2 / Biso mean: 45.07 Å2 / Biso min: 22.74 Å2
Baniso -1Baniso -2Baniso -3
1-4.1996 Å20 Å20 Å2
2--5.56 Å20 Å2
3----9.7596 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.35→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 10 95 3204
Biso mean--92.13 44.26 -
Num. residues----405
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1081SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it3165HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3446SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3165HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4297HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion17.1
LS refinement shellResolution: 2.35→2.46 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2986 130 4.85 %
Rwork0.2564 2550 -
all0.2584 2680 -
obs--97.07 %
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)
13.3791-1.05621.31152.45371.55572.93720.00770.0556-0.0057-0.11960.0014-0.22130.01160.0326-0.0091-0.04570.04970.0074-0.0771-0.0003-0.00228.6474-13.338129.6663
21.9641-0.54781.18713.91811.27414.32170.0176-0.0664-0.13510.0122-0.015-0.0393-0.0361-0.0253-0.0026-0.08740.028-0.0244-0.0709-0.0170.0009-24.6995-9.126619.8044
30.91090.46641.08035.2222-1.41711.2012-0.0062-0.15390.13260.032-0.0113-0.0272-0.0073-0.08580.0175-0.14130.0336-0.0587-0.0428-0.03560.0183-8.94288.344833.0226
45.49820.0529-0.86792.20240.66511.0104-0.00550.04640.0051-0.11570.0110.13560.00890.0382-0.0055-0.0060.076-0.0487-0.0947-0.0571-0.0848-10.3753-27.401616.4635
50.2572-0.23980.10570.16690.18090.14480.00080.00160.0063-0.00590.0002-0.0094-0.00790.0007-0.0010.01550.02340.0266-0.01110.00890.0112.2771-6.841823.1698
60.1524-0.25130.21790.360.34160.2983-0.0013-0.004-0.005-0.0001-0.00020.0112-0.0062-0.00020.00150.01250.01010.02060.02090.0169-0.017-30.6445-1.876626.1473
70.3196-0.4795-0.03110.45440.60880.375-0.0013-0.00230.0126-0.01960.0028-0.00020.00020.0077-0.00150.0080.0427-0.05040.0266-0.0484-0.025-2.9887-4.06544.0011
80.7938-0.48810.42770.0068-0.41970.2515-0.0042-0.0147-0.0021-0.01790.00760.0024-0.0051-0.0059-0.00340.02240.08520.0057-0.0091-0.0284-0.00081.5919-34.74075.6342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA511 - 604
2X-RAY DIFFRACTION2CHAIN BB510 - 604
3X-RAY DIFFRACTION3CHAIN CC511 - 604
4X-RAY DIFFRACTION4CHAIN DD510 - 604
5X-RAY DIFFRACTION5CHAIN EE8 - 13
6X-RAY DIFFRACTION6CHAIN FF8 - 13
7X-RAY DIFFRACTION7CHAIN GG3 - 13
8X-RAY DIFFRACTION8CHAIN HH3 - 13

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