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- PDB-6iwd: The PTP domain of human PTPN14 in a complex with the CR3 domain o... -

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Basic information

Entry
Database: PDB / ID: 6iwd
TitleThe PTP domain of human PTPN14 in a complex with the CR3 domain of HPV18 E7
Components
  • HPV18 E7
  • Tyrosine-protein phosphatase non-receptor type 14
KeywordsONCOPROTEIN
Function / homology
Function and homology information


lymphangiogenesis / regulation of protein export from nucleus / Interleukin-37 signaling / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / transcription coregulator activity / receptor tyrosine kinase binding / host cell cytoplasm ...lymphangiogenesis / regulation of protein export from nucleus / Interleukin-37 signaling / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / transcription coregulator activity / receptor tyrosine kinase binding / host cell cytoplasm / cytoskeleton / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Double Stranded RNA Binding Domain - #330 / Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / Papillomavirus E7 / E7 protein, Early protein / 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 ...Double Stranded RNA Binding Domain - #330 / Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / Papillomavirus E7 / E7 protein, Early protein / 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 / Protein tyrosine phosphatase superfamily / Double Stranded RNA Binding Domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Protein-Tyrosine Phosphatase; Chain A / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein E7 / Tyrosine-protein phosphatase non-receptor type 14 / Protein E7
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYun, H.-Y. / Kim, S.J. / Ku, B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015M3A9B5030308 Korea, Republic Of
CitationJournal: Plos Biol. / Year: 2019
Title: Structural basis for recognition of the tumor suppressor protein PTPN14 by the oncoprotein E7 of human papillomavirus.
Authors: Yun, H.Y. / Kim, M.W. / Lee, H.S. / Kim, W. / Shin, J.H. / Kim, H. / Shin, H.C. / Park, H. / Oh, B.H. / Kim, W.K. / Bae, K.H. / Lee, S.C. / Lee, E.W. / Ku, B. / Kim, S.J.
History
DepositionDec 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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 14
B: HPV18 E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6376
Polymers41,3472
Non-polymers2914
Water4,828268
1
A: Tyrosine-protein phosphatase non-receptor type 14
B: HPV18 E7
hetero molecules

A: Tyrosine-protein phosphatase non-receptor type 14
B: HPV18 E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,27512
Polymers82,6934
Non-polymers5828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6080 Å2
ΔGint-58 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.573, 169.153, 42.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-338-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Tyrosine-protein phosphatase non-receptor type 14 / Protein-tyrosine phosphatase pez


Mass: 35063.305 Da / Num. of mol.: 1 / Fragment: UNP residues 886-1187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15678, protein-tyrosine-phosphatase
#2: Protein HPV18 E7


Mass: 6283.309 Da / Num. of mol.: 1 / Fragment: UNP residues 54-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Gene: E7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76Z96, UniProt: P06788*PLUS

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Non-polymers , 4 types, 272 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 8.0, 25% (w/v) polyethylene glycol 3350, 0.25 M lithium sulfate monohydrate, and 2% (v/v) tert-butanol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35719 / % possible obs: 95.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 41.3
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.328 / Num. unique obs: 1615

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Processing

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

2bzl


Resolution: 1.8→29.987 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.2125 2000 5.61 %
Rwork0.1858 --
obs0.1873 35674 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 12 268 2964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072759
X-RAY DIFFRACTIONf_angle_d0.7743737
X-RAY DIFFRACTIONf_dihedral_angle_d19.3171649
X-RAY DIFFRACTIONf_chiral_restr0.055413
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.84480.31951300.27692189X-RAY DIFFRACTION88
1.8448-1.89470.26791300.23972180X-RAY DIFFRACTION89
1.8947-1.95050.24351330.22022244X-RAY DIFFRACTION89
1.9505-2.01340.26641330.20092243X-RAY DIFFRACTION90
2.0134-2.08530.23531360.19962292X-RAY DIFFRACTION93
2.0853-2.16880.23631410.18732370X-RAY DIFFRACTION94
2.1688-2.26750.23541430.18372392X-RAY DIFFRACTION96
2.2675-2.3870.24811450.18312466X-RAY DIFFRACTION98
2.387-2.53650.22751470.18872477X-RAY DIFFRACTION99
2.5365-2.73220.21851510.19692518X-RAY DIFFRACTION99
2.7322-3.00690.23251500.20382536X-RAY DIFFRACTION100
3.0069-3.44150.20621510.18742540X-RAY DIFFRACTION100
3.4415-4.33380.17471540.15822589X-RAY DIFFRACTION100
4.3338-29.99160.18041560.16832638X-RAY DIFFRACTION97

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