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

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Basic information

Entry
Database: PDB / ID: 3nfk
TitleCrystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies virus G protein
Components
  • Glycoprotein G
  • Tyrosine-protein phosphatase non-receptor type 4
KeywordsPROTEIN BINDING / PDZ-PDZ-binding site complex
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 / viral envelope / virion membrane / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / 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 ...Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / 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
Glycoprotein / Tyrosine-protein phosphatase non-receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Rabies virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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: Glycoprotein G
D: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5266
Polymers26,3424
Non-polymers1842
Water3,261181
1
A: Tyrosine-protein phosphatase non-receptor type 4
C: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3554
Polymers13,1712
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-2 kcal/mol
Surface area6040 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 4
D: Glycoprotein G


Theoretical massNumber of molelcules
Total (without water)13,1712
Polymers13,1712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-3 kcal/mol
Surface area5880 Å2
MethodPISA
3
C: Glycoprotein G

A: Tyrosine-protein phosphatase non-receptor type 4
B: Tyrosine-protein phosphatase non-receptor type 4
D: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5266
Polymers26,3424
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 53.700, 81.800
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.: 2 / 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 Glycoprotein G


Mass: 1476.572 Da / Num. of mol.: 2 / Fragment: UNP residues 512-524 / Source method: obtained synthetically
Details: Cyto13-att peptide has been chemically synthetized. The sequence occurs naturally in rabies virus G protein
Source: (synth.) Rabies virus / References: UniProt: P03524
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 24% PEG 1500, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2009 / Details: BI-MORPH MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.43→34.37 Å / Num. all: 44164 / Num. obs: 42795 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.28 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6255 / % possible all: 98.5

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Processing

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

2vph


Resolution: 1.43→14.41 Å / Cor.coef. Fo:Fc: 0.9495 / Cor.coef. Fo:Fc free: 0.9447 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 2155 5.05 %RANDOM
Rwork0.1921 ---
obs0.1927 42710 96.7 %-
all-44167 --
Displacement parametersBiso mean: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.2203 Å20 Å20 Å2
2--0.7572 Å20 Å2
3---0.4631 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: LAST / Resolution: 1.43→14.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 12 181 1741
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0116002
X-RAY DIFFRACTIONt_angle_deg1.1421602
X-RAY DIFFRACTIONt_dihedral_angle_d5792
X-RAY DIFFRACTIONt_trig_c_planes472
X-RAY DIFFRACTIONt_gen_planes2325
X-RAY DIFFRACTIONt_it160020
X-RAY DIFFRACTIONt_omega_torsion4.1
X-RAY DIFFRACTIONt_other_torsion13.85
X-RAY DIFFRACTIONt_chiral_improper_torsion2015
X-RAY DIFFRACTIONt_ideal_dist_contact19764
LS refinement shellResolution: 1.43→1.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2333 159 5.03 %
Rwork0.1853 3001 -
all0.1876 3160 -
obs--96.7 %
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)
11.05550.0333-0.06721.2897-0.06270.6118-0.00580.02090.0121-0.01720.0061-0.13310.00050.0419-0.0003-0.07480.0017-0.0011-0.04640.008-0.037933.1435-18.505615.3124
22.1534-0.8889-1.12093.4346-0.22641.74660.03930.15370.0018-0.1086-0.02410.22860.0717-0.1022-0.0152-0.02-0.0048-0.0143-0.0039-0.00580.005624.426-9.423618.0277
31.4659-1.37150.20313.2971-1.00751.8874-0.0566-0.06670.07310.02110.15810.0588-0.1304-0.131-0.1014-0.0365-0.0055-0.00060.01880.0221-0.015427.3935-1.7889-5.2299
40.02070.3334-0.89130-0.11620.3054-0.016-0.01450.03080.0268-0.0158-0.0154-0.03310.01320.03180.02330.03-0.02070.0082-0.0216-0.03234.6611.00372.366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|513 - A|604 }A513 - 604
2X-RAY DIFFRACTION2{ C|1 - C|13 }C1 - 13
3X-RAY DIFFRACTION3{ B|512 - B|591 B|594 - B|604 }B512 - 591
4X-RAY DIFFRACTION3{ B|512 - B|591 B|594 - B|604 }B594 - 604
5X-RAY DIFFRACTION4{ D|9 - D|13 }D9 - 13

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