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- PDB-7vze: Crystal structure of PTPN4 PDZ bound to the PBM of HPV16 E6 -

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Basic information

Entry
Database: PDB / ID: 7vze
TitleCrystal structure of PTPN4 PDZ bound to the PBM of HPV16 E6
Components
  • Tyrosine-protein phosphatase non-receptor type 4
  • the PDZ-binding motif of HPV16 E6
KeywordsPROTEIN BINDING / PTPN4 / PDZ / HPV16 / human papillomavirus / E6. PBM / 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 / 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
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.882 Å
AuthorsLee, H.S. / Yun, H.-Y. / Ku, B.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1C1C1008451 Korea, Republic Of
National Research Foundation (NRF, Korea)2019M3E5D6063955 Korea, Republic Of
National Research Foundation (NRF, Korea)KGM9952112 Korea, Republic Of
CitationJournal: J.Microbiol / Year: 2022
Title: Structural and biochemical analysis of the PTPN4 PDZ domain bound to the C-terminal tail of the human papillomavirus E6 oncoprotein.
Authors: Lee, H.S. / Yun, H.Y. / Lee, E.W. / Shin, H.C. / Kim, S.J. / Ku, B.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: the PDZ-binding motif of HPV16 E6
F: the PDZ-binding motif of HPV16 E6
G: the PDZ-binding motif of HPV16 E6
H: the PDZ-binding motif of HPV16 E6


Theoretical massNumber of molelcules
Total (without water)45,4128
Polymers45,4128
Non-polymers00
Water25214
1
A: Tyrosine-protein phosphatase non-receptor type 4
E: the PDZ-binding motif of HPV16 E6


Theoretical massNumber of molelcules
Total (without water)11,3532
Polymers11,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 4
F: the PDZ-binding motif of HPV16 E6


Theoretical massNumber of molelcules
Total (without water)11,3532
Polymers11,3532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase non-receptor type 4
G: the PDZ-binding motif of HPV16 E6


Theoretical massNumber of molelcules
Total (without water)11,3532
Polymers11,3532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein phosphatase non-receptor type 4
H: the PDZ-binding motif of HPV16 E6


Theoretical massNumber of molelcules
Total (without water)11,3532
Polymers11,3532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.973, 51.916, 190.968
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 / MEG / PTPase-MEG1


Mass: 10448.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN4 / Production host: Escherichia coli (E. coli) / References: UniProt: P29074, protein-tyrosine-phosphatase
#2: Protein/peptide
the PDZ-binding motif of HPV16 E6


Mass: 905.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.15M calcium acetate hydrate, 24% (w/v) polyethylene glycol 3350, 4.5% w/v trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.48
ReflectionResolution: 2.882→50 Å / Num. obs: 12140 / % possible obs: 99.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 21.6
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.28 / Num. unique obs: 554

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPH

2vph


Resolution: 2.882→47.742 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2343 1229 10.12 %
Rwork0.1949 --
obs0.2046 12140 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.882→47.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 0 14 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112971
X-RAY DIFFRACTIONf_angle_d1.0584014
X-RAY DIFFRACTIONf_dihedral_angle_d16.2481844
X-RAY DIFFRACTIONf_chiral_restr0.055464
X-RAY DIFFRACTIONf_plane_restr0.006534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8861-3.00160.32221180.27321101X-RAY DIFFRACTION84
3.0016-3.13810.32851350.26691197X-RAY DIFFRACTION90
3.1381-3.30350.28841400.24091204X-RAY DIFFRACTION90
3.3035-3.51030.25181350.24081203X-RAY DIFFRACTION90
3.5103-3.78110.26111300.20341184X-RAY DIFFRACTION89
3.7811-4.16110.26311340.19321214X-RAY DIFFRACTION90
4.1611-4.76210.20981350.17181243X-RAY DIFFRACTION90
4.7621-5.99550.20941410.15911239X-RAY DIFFRACTION90
5.9955-36.73320.22411540.18941319X-RAY DIFFRACTION89

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