[English] 日本語
Yorodumi
- PDB-6iwd: The PTP domain of human PTPN14 in a complex with the CR3 domain o... -

+
Open data


ID or keywords:

Loading...

-
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 / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA-binding transcription factor activity / negative regulation of cell population proliferation / protein domain specific binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / 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 / Protein tyrosine phosphatase superfamily / FERM central domain / Double Stranded RNA Binding Domain / FERM superfamily, second domain / Protein-Tyrosine Phosphatase; Chain A / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 4 types, 272 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more