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

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Basic information

Entry
Database: PDB / ID: 5eyz
TitleCRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE TAILORED PEPTIDE CYTO8-RETEV
Components
  • CYTO8-RETEV
  • Tyrosine-protein phosphatase non-receptor type 4
KeywordsAPOPTOSIS / CELL DEATH / GLIOBLASTOMA / MULTIPROTEIN COMPLEXES / PDZ DOMAINS / PEPTIDES DESIGN / 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 / 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 ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase 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 / 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. / 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 / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMaisonneuve, P. / Vaney, M.C. / Babault, B. / 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 1.3Oct 19, 2016Group: Refinement description
Revision 1.4Dec 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 1.5Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.6Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: CYTO8-RETEV
F: CYTO8-RETEV
G: CYTO8-RETEV
H: CYTO8-RETEV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9519
Polymers52,9168
Non-polymers351
Water1,964109
1
A: Tyrosine-protein phosphatase non-receptor type 4
E: CYTO8-RETEV


Theoretical massNumber of molelcules
Total (without water)13,2292
Polymers13,2292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 4
F: CYTO8-RETEV


Theoretical massNumber of molelcules
Total (without water)13,2292
Polymers13,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase non-receptor type 4
G: CYTO8-RETEV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2643
Polymers13,2292
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein phosphatase non-receptor type 4
H: CYTO8-RETEV


Theoretical massNumber of molelcules
Total (without water)13,2292
Polymers13,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.710, 80.880, 170.230
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(0.8949, 0.4462, 0.01154), (-0.4461, -0.8931, -0.05842), (-0.01576, -0.05742, 0.9982)63.130001, -65.959999, 0.4525
2given(-0.04644, -0.9988, 0.01462), (-0.9988, 0.04667, 0.01623), (-0.01689, -0.01384, -0.9998)-0.3017, -38.889999, -42.939999
3given(-0.4185, 0.9082, 0.004394), (0.9067, 0.4175, 0.06086), (0.05344, 0.02945, -0.9981)45.880001, -27.879999, -39.310001

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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) / Variant (production host): Star / References: UniProt: P29074, protein-tyrosine-phosphatase
#2: Protein/peptide
CYTO8-RETEV


Mass: 1534.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 23% PEG 8000, 0.1 M MES PH 6.0, 0.2 M CALCIUM ACETATE, 0.143 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28268 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2011
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28268 Å / Relative weight: 1
ReflectionResolution: 2.09→46.8 Å / Num. all: 30269 / Num. obs: 30269 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 54.44 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.025 / Rrim(I) all: 0.056 / Net I/av σ(I): 6.39 / Net I/σ(I): 14.2 / Num. measured all: 141532
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / Num. measured all: 4830 / Num. unique all: 1120 / Rpim(I) all: 0.022 / Net I/σ(I) obs: 31.2 / Rejects: 0 / % possible all: 63

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.2refinement
SCALA3.3.9data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NFK

3nfk


Resolution: 2.09→42.56 Å / Cor.coef. Fo:Fc: 0.9419 / Cor.coef. Fo:Fc free: 0.9452 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.165
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1539 5.09 %RANDOM
Rwork0.2291 ---
obs0.2297 30234 94.02 %-
Displacement parametersBiso max: 141.04 Å2 / Biso mean: 65.36 Å2 / Biso min: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.7697 Å20 Å20 Å2
2--3.324 Å20 Å2
3----11.0937 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: final / Resolution: 2.09→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 1 109 3176
Biso mean--100.5 63.88 -
Num. residues----396
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1116SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes446HARMONIC5
X-RAY DIFFRACTIONt_it3111HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion392SEMIHARMONIC5
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_contact3393SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3111HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg4204HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion17.29
LS refinement shellResolution: 2.09→2.16 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2926 80 4.79 %
Rwork0.2377 1590 -
all0.2402 1670 -
obs--94.02 %
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)
16.48522.2317-0.44655.9905-0.55374.18840.0811-0.13330.07040.0038-0.2199-0.4179-0.16170.09220.1388-0.1847-0.0031-0.0059-0.15590.0674-0.079228.7617-27.2673-16.3857
27.265-0.59850.64635.375-0.93895.5812-0.00830.0290.0477-0.27830.03590.54430.0261-0.1881-0.0276-0.14590.01190.0039-0.10770.0199-0.043413.7677-49.195-19.3946
38.15951.6540.23534.9833-0.58464.3574-0.0145-0.0128-0.5443-0.20550.10110.08240.4365-0.095-0.0866-0.1586-0.02210.046-0.2018-0.0193-0.078-13.4567-28.8054-25.8674
46.9960.1178-1.32365.70031.27246.76610.0936-0.07440.5444-0.0169-0.04250.106-0.21660.0871-0.0511-0.14330.02950.0102-0.1640.0165-0.00698.8189-14.6376-22.9217
50.3308-0.217-0.07290.6544-0.361400.0049-0.0602-0.00280.0469-0.0069-0.013-0.01050.00560.002-0.0205-0.0126-0.0489-0.00620.05480.03534.9217-33.8594-9.25
60.3775-0.1053-0.17210.36770.41730.07560.0078-0.0591-0.00170.0362-0.01040.02130.0009-0.020.0026-0.03690.08250.0735-0.0131-0.04770.059711.4101-40.7599-12.0495
70.382-0.5769-0.47680.13860.24340.0129-0.00140.0372-0.0208-0.03130.0090.00860.0113-0.0082-0.0075-0.0030.06590.0491-0.0242-0.12660.033-7.2119-35.3199-33.1895
80.0997-0.43840.47250.33870.03480.0004-0.00020.04760.0133-0.07020.00430.0121-0.02040.0025-0.0041-0.03170.1038-0.0379-0.03860.08020.080.8818-11.8718-30.2823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA512 - 604
2X-RAY DIFFRACTION2CHAIN BB511 - 604
3X-RAY DIFFRACTION3CHAIN CC512 - 604
4X-RAY DIFFRACTION4CHAIN DD513 - 604
5X-RAY DIFFRACTION5CHAIN EE8 - 13
6X-RAY DIFFRACTION6CHAIN FF8 - 13
7X-RAY DIFFRACTION7CHAIN GG8 - 13
8X-RAY DIFFRACTION8CHAIN HH8 - 13

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