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- PDB-3nfl: Crystal structure of the PTPN4 PDZ domain complexed with the C-te... -

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Basic information

Entry
Database: PDB / ID: 3nfl
TitleCrystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit
Components
  • Glutamate [NMDA] receptor subunit epsilon-1
  • Tyrosine-protein phosphatase non-receptor type 4
KeywordsPROTEIN BINDING / PDZ-PDZ-binding site complex
Function / homology
Function and homology information


excitatory chemical synaptic transmission / Toll Like Receptor 4 (TLR4) Cascade / directional locomotion / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / serotonin metabolic process / Interleukin-37 signaling / sleep / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport ...excitatory chemical synaptic transmission / Toll Like Receptor 4 (TLR4) Cascade / directional locomotion / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / serotonin metabolic process / Interleukin-37 signaling / sleep / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / startle response / monoatomic cation transmembrane transport / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / non-membrane spanning protein tyrosine phosphatase activity / Long-term potentiation / regulation of neuronal synaptic plasticity / glutamate receptor binding / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / protein dephosphorylation / cytoskeletal protein binding / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / neurogenesis / protein-tyrosine-phosphatase / sensory perception of pain / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / protein tyrosine phosphatase activity / cytoplasmic vesicle membrane / synaptic membrane / response to amphetamine / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / protein catabolic process / postsynaptic density membrane / brain development / negative regulation of protein catabolic process / visual learning / regulation of synaptic plasticity / calcium ion transmembrane transport / response to wounding / memory / cytoplasmic side of plasma membrane / long-term synaptic potentiation / synaptic vesicle / amyloid-beta binding / presynaptic membrane / response to ethanol / dendritic spine / chemical synaptic transmission / postsynaptic membrane / learning or memory / cytoskeleton / postsynaptic density / positive regulation of apoptotic process / response to xenobiotic stimulus / endoplasmic reticulum membrane / glutamatergic synapse / cell surface / zinc ion binding / nucleoplasm / plasma membrane / 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. / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PDZ domain / FERM central domain / Pdz3 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / PDZ domain / Receptor, ligand binding region / Receptor family ligand binding region / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Periplasmic binding protein-like I / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 4 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBabault, N. / Cordier, F. / Lafage, M. / Cockburn, J. / Haouz, A. / Rey, F.A. / Delepierre, M. / Buc, H. / Lafon, M. / Wolff, N.
CitationJournal: 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
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 6, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Glutamate [NMDA] receptor subunit epsilon-1
F: Glutamate [NMDA] receptor subunit epsilon-1
G: Glutamate [NMDA] receptor subunit epsilon-1
H: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)54,4308
Polymers54,4308
Non-polymers00
Water3,009167
1
A: Tyrosine-protein phosphatase non-receptor type 4
E: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)13,6082
Polymers13,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-2 kcal/mol
Surface area5830 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 4
F: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)13,6082
Polymers13,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-2 kcal/mol
Surface area5730 Å2
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 4
G: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)13,6082
Polymers13,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-2 kcal/mol
Surface area5590 Å2
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 4
H: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)13,6082
Polymers13,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-3 kcal/mol
Surface area5520 Å2
MethodPISA
5
A: Tyrosine-protein phosphatase non-receptor type 4
E: Glutamate [NMDA] receptor subunit epsilon-1

D: Tyrosine-protein phosphatase non-receptor type 4
H: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)27,2154
Polymers27,2154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area2680 Å2
ΔGint-12 kcal/mol
Surface area10250 Å2
MethodPISA
6
B: Tyrosine-protein phosphatase non-receptor type 4
F: Glutamate [NMDA] receptor subunit epsilon-1

C: Tyrosine-protein phosphatase non-receptor type 4
G: Glutamate [NMDA] receptor subunit epsilon-1


Theoretical massNumber of molelcules
Total (without water)27,2154
Polymers27,2154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area2700 Å2
ΔGint-13 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.582, 51.679, 190.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 11694.363 Da / Num. of mol.: 4 / Fragment: PDZ domain (UNP 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 (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P29074
#2: Protein/peptide
Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A / hNR2A


Mass: 1913.204 Da / Num. of mol.: 4 / Fragment: UNP residues 1449-1464 / Source method: obtained synthetically
Details: NR2A16 peptide has been chemically synthetized. The sequence ocuurs naturally in Homo sapiens (Human)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q12879
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2009
RadiationMonochromator: LN2 cooled fixed-exit Si(111) Dynamically bendable mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→95.45 Å / Num. all: 40560 / Num. obs: 38978 / % possible obs: 96.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.1
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2 / Num. unique all: 4287 / % possible all: 74.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VPH

2vph


Resolution: 1.91→49.88 Å / Cor.coef. Fo:Fc: 0.9235 / Cor.coef. Fo:Fc free: 0.9025 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1959 5.03 %RANDOM
Rwork0.2166 ---
obs0.218 38911 95.84 %-
all-40490 --
Displacement parametersBiso mean: 54.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.876 Å20 Å20 Å2
2---6.5161 Å20 Å2
3---5.6401 Å2
Refine analyzeLuzzati coordinate error obs: 0.387 Å
Refinement stepCycle: LAST / Resolution: 1.91→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 0 167 3091
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0129942
X-RAY DIFFRACTIONt_angle_deg1.1840542
X-RAY DIFFRACTIONt_dihedral_angle_d10612
X-RAY DIFFRACTIONt_trig_c_planes922
X-RAY DIFFRACTIONt_gen_planes4275
X-RAY DIFFRACTIONt_it299420
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion18.12
X-RAY DIFFRACTIONt_chiral_improper_torsion3835
X-RAY DIFFRACTIONt_ideal_dist_contact34074
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2541 100 5.13 %
Rwork0.2099 1849 -
all0.2122 1949 -
obs--95.84 %
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)
18.3155-2.04651.28925.31780.11376.12080.25360.5442-0.17860.0172-0.2906-0.27850.06470.16070.037-0.2163-0.00560.03480.1952-0.0206-0.256815.2227-13.6259-13.2444
20.7230.5207-0.841200.05660.4035-0.01060.06750.05010.0376-0.03330.0001-0.05280.02350.0439-0.1793-0.062-0.08480.18580.1230.014225.1678-9.7598-10.7435
31.67120.04130.51165.4487-0.25384.90150.2107-0.178-0.06390.5442-0.33350.0459-0.3474-0.26330.12280.2038-0.1074-0.0694-0.15030.0184-0.1166-0.86823.966559.2921
40-0.4521.32770.0377-2.33141.1841-0.01110.0025-0.0110.0964-0.08140.0748-0.02340.04680.09260.0854-0.1292-0.0814-0.09260.02190.0276-4.938214.952655.9402
51.30860.290.87454.41140.38895.90770.22350.0934-0.0009-0.4322-0.21260.03160.4339-0.04-0.0110.14220.0768-0.0592-0.21830.0124-0.1706-1.112821.989833.2558
67.6290.433-2.91041.2705-0.62947.9913-0.0248-0.04220.287-0.02140.5195-0.092-0.13840.5442-0.4947-0.2206-0.11550.01830.304-0.0432-0.30417.1771-11.247813.0444
70-0.65510.63050.34540.06770.1177-0.00090.01640.0131-0.0325-0.01760.13720.0219-0.06110.01860.1830.0747-0.1082-0.0427-0.0044-0.1184-5.855931.741733.5772
80-0.66040.64470.0696-0.0150-0.0102-0.02160.0456-0.0201-0.00550.0172-0.0368-0.0070.0157-0.1258-0.0516-0.06840.27890.152-0.13137.3425-7.792911.1394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|511 - C|590 C|596 - C|604 }C511 - 590
2X-RAY DIFFRACTION1{ C|511 - C|590 C|596 - C|604 }C596 - 604
3X-RAY DIFFRACTION2{ G|12 - G|16 }G12 - 16
4X-RAY DIFFRACTION3{ D|513 - D|591 D|595 - D|604 }D513 - 591
5X-RAY DIFFRACTION3{ D|513 - D|591 D|595 - D|604 }D595 - 604
6X-RAY DIFFRACTION4{ H|12 - H|16 }H12 - 16
7X-RAY DIFFRACTION5{ A|512 - A|603 }A512 - 603
8X-RAY DIFFRACTION6{ B|512 - B|590 B|594 - B|603 }B512 - 590
9X-RAY DIFFRACTION6{ B|512 - B|590 B|594 - B|603 }B594 - 603
10X-RAY DIFFRACTION7{ E|12 - E|16 }E12 - 16
11X-RAY DIFFRACTION8{ F|12 - F|16 }F12 - 16

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