[English] 日本語
Yorodumi
- PDB-5mk3: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mk3
TitleCrystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro 1 domain (CHMP4C peptide complex structure)
Components
  • Charged multivesicular body protein 4c
  • Tyrosine-protein phosphatase non-receptor type 23
KeywordsHYDROLASE / ESCRT-III CHMP4C
Function / homology
Function and homology information


positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole ...positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / negative regulation of epithelial cell migration / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / early endosome to late endosome transport / Sealing of the nuclear envelope (NE) by ESCRT-III / multivesicular body sorting pathway / midbody abscission / membrane fission / plasma membrane repair / vesicle budding from membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / multivesicular body membrane / endocytic recycling / Interleukin-37 signaling / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Flemming body / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / cilium assembly / autophagosome maturation / Pyroptosis / nuclear pore / multivesicular body / protein-tyrosine-phosphatase / Endosomal Sorting Complex Required For Transport (ESCRT) / protein tyrosine phosphatase activity / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / centriolar satellite / cytoplasmic side of plasma membrane / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / early endosome / endosome / nuclear body / ciliary basal body / lysosomal membrane / intracellular membrane-bounded organelle / protein kinase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family / Snf7 ...alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family / Snf7 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Charged multivesicular body protein 4c / Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLevy, C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701140 United Kingdom
Medical Research Council (United Kingdom)MR/K011049/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K008773/1 United Kingdom
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Specific Interaction of TGF beta Signaling Regulators SARA/Endofin with HD-PTP.
Authors: Gahloth, D. / Levy, C. / Walker, L. / Wunderley, L. / Mould, A.P. / Taylor, S. / Woodman, P. / Tabernero, L.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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 23
B: Tyrosine-protein phosphatase non-receptor type 23
C: Tyrosine-protein phosphatase non-receptor type 23
D: Tyrosine-protein phosphatase non-receptor type 23
E: Charged multivesicular body protein 4c
F: Charged multivesicular body protein 4c
G: Charged multivesicular body protein 4c
H: Charged multivesicular body protein 4c


Theoretical massNumber of molelcules
Total (without water)171,2458
Polymers171,2458
Non-polymers00
Water14,052780
1
A: Tyrosine-protein phosphatase non-receptor type 23
E: Charged multivesicular body protein 4c


Theoretical massNumber of molelcules
Total (without water)42,8112
Polymers42,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area16500 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 23
F: Charged multivesicular body protein 4c


Theoretical massNumber of molelcules
Total (without water)42,8112
Polymers42,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-7 kcal/mol
Surface area16720 Å2
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 23
G: Charged multivesicular body protein 4c


Theoretical massNumber of molelcules
Total (without water)42,8112
Polymers42,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area16620 Å2
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 23
H: Charged multivesicular body protein 4c


Theoretical massNumber of molelcules
Total (without water)42,8112
Polymers42,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.436, 70.835, 79.291
Angle α, β, γ (deg.)90.54, 98.22, 106.82
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Tyrosine-protein phosphatase non-receptor type 23 / His domain-containing protein tyrosine phosphatase / HD-PTP / Protein tyrosine phosphatase TD14 / PTP-TD14


Mass: 40719.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase
#2: Protein/peptide
Charged multivesicular body protein 4c / Chromatin-modifying protein 4c / CHMP4c / SNF7 homolog associated with Alix 3 / SNF7-3 / hSnf7-3 / ...Chromatin-modifying protein 4c / CHMP4c / SNF7 homolog associated with Alix 3 / SNF7-3 / hSnf7-3 / Vacuolar protein sorting-associated protein 32-3 / hVps32-3


Mass: 2091.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CF2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→49.92 Å / Num. obs: 88613 / % possible obs: 95.87 % / Redundancy: 2.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0567 / Net I/σ(I): 11.96
Reflection shellResolution: 2→2.071 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.22 / CC1/2: 0.949 / % possible all: 94.24

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2563: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAU

3rau


Resolution: 2→49.92 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.235 1444 1.63 %
Rwork0.1975 --
obs0.1982 88588 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11762 0 0 780 12542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212061
X-RAY DIFFRACTIONf_angle_d0.53516304
X-RAY DIFFRACTIONf_dihedral_angle_d1.97210197
X-RAY DIFFRACTIONf_chiral_restr0.0381777
X-RAY DIFFRACTIONf_plane_restr0.0032115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.32991430.26138571X-RAY DIFFRACTION94
2.0715-2.15440.28651360.24618561X-RAY DIFFRACTION94
2.1544-2.25250.271430.23428537X-RAY DIFFRACTION94
2.2525-2.37120.29811450.23048724X-RAY DIFFRACTION96
2.3712-2.51980.27621460.22358721X-RAY DIFFRACTION96
2.5198-2.71430.30141480.22238841X-RAY DIFFRACTION97
2.7143-2.98750.23571460.21598834X-RAY DIFFRACTION97
2.9875-3.41970.23151420.20238808X-RAY DIFFRACTION97
3.4197-4.3080.19881470.16238796X-RAY DIFFRACTION97
4.308-49.93930.18261480.16058751X-RAY DIFFRACTION96

+
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