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- PDB-5mk2: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -

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Basic information

Entry
Database: PDB / ID: 5mk2
TitleCrystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4B peptide complex structure)
Components
  • Charged multivesicular body protein 4b
  • Tyrosine-protein phosphatase non-receptor type 23
KeywordsHYDROLASE / ESCRT-III CHMP4B
Function / homology
Function and homology information


positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / post-translational protein targeting to endoplasmic reticulum membrane / multivesicular body sorting pathway / vesicle budding from membrane / membrane fission / plasma membrane repair / membrane coat / early endosome to late endosome transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / exit from mitosis / multivesicular body assembly / regulation of mitotic spindle assembly / endocytic recycling / nervous system process / Translation of Replicase and Assembly of the Replication Transcription Complex / Interleukin-37 signaling / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / mitotic cytokinesis / cilium assembly / protein polymerization / Pyroptosis / nuclear pore / dephosphorylation / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / protein-tyrosine-phosphatase / viral budding from plasma membrane / ciliary basal body / HCMV Late Events / protein tyrosine phosphatase activity / regulation of autophagy / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / cytoplasmic side of plasma membrane / kinetochore / autophagy / protein transport / nuclear envelope / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / vesicle / early endosome / nuclear body / endosome / cadherin binding / lysosomal membrane / intracellular membrane-bounded organelle / protein kinase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / 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 ...alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 23 / Charged multivesicular body protein 4b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLevy, C. / Gahloth, D.
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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 23
B: Tyrosine-protein phosphatase non-receptor type 23
C: Charged multivesicular body protein 4b


Theoretical massNumber of molelcules
Total (without water)83,8573
Polymers83,8573
Non-polymers00
Water11,998666
1
A: Tyrosine-protein phosphatase non-receptor type 23


Theoretical massNumber of molelcules
Total (without water)40,7201
Polymers40,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16320 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 23
C: Charged multivesicular body protein 4b


Theoretical massNumber of molelcules
Total (without water)43,1372
Polymers43,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.440, 64.860, 81.230
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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 4b / Chromatin-modifying protein 4b / CHMP4b / SNF7 homolog associated with Alix 1 / SNF7-2 / hSnf7-2 / ...Chromatin-modifying protein 4b / CHMP4b / SNF7 homolog associated with Alix 1 / SNF7-2 / hSnf7-2 / Vacuolar protein sorting-associated protein 32-2 / hVps32-2


Mass: 2416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H444
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% PEG 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50.685 Å / Num. all: 251418 / Num. obs: 77355 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.56

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Processing

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

3rau


Resolution: 1.7→50.685 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.09
RfactorNum. reflection% reflection
Rfree0.2032 3700 4.78 %
Rwork0.1692 --
obs0.1708 77351 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→50.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 0 0 666 6423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065969
X-RAY DIFFRACTIONf_angle_d0.7488075
X-RAY DIFFRACTIONf_dihedral_angle_d3.285050
X-RAY DIFFRACTIONf_chiral_restr0.047873
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72240.2581390.2252629X-RAY DIFFRACTION93
1.7224-1.7460.27951450.21362747X-RAY DIFFRACTION96
1.746-1.77090.24361310.21352820X-RAY DIFFRACTION99
1.7709-1.79730.251530.1992855X-RAY DIFFRACTION100
1.7973-1.82540.27671430.1952845X-RAY DIFFRACTION100
1.8254-1.85540.24531420.18672881X-RAY DIFFRACTION100
1.8554-1.88740.24611150.18242887X-RAY DIFFRACTION100
1.8874-1.92170.25511550.18122800X-RAY DIFFRACTION100
1.9217-1.95860.21681560.18282859X-RAY DIFFRACTION100
1.9586-1.99860.23091390.18392846X-RAY DIFFRACTION100
1.9986-2.04210.24141390.17892870X-RAY DIFFRACTION100
2.0421-2.08960.18471350.17732850X-RAY DIFFRACTION100
2.0896-2.14180.20251290.16582858X-RAY DIFFRACTION100
2.1418-2.19980.23961320.16292837X-RAY DIFFRACTION99
2.1998-2.26450.2341470.16412881X-RAY DIFFRACTION99
2.2645-2.33760.17531440.16642796X-RAY DIFFRACTION99
2.3376-2.42110.19191380.16692879X-RAY DIFFRACTION99
2.4211-2.51810.17541530.16462827X-RAY DIFFRACTION99
2.5181-2.63270.21361610.16562837X-RAY DIFFRACTION99
2.6327-2.77140.22061570.16962817X-RAY DIFFRACTION99
2.7714-2.94510.19761330.17452851X-RAY DIFFRACTION98
2.9451-3.17240.21171020.182829X-RAY DIFFRACTION98
3.1724-3.49160.2051520.16792820X-RAY DIFFRACTION98
3.4916-3.99670.18071320.14842843X-RAY DIFFRACTION98
3.9967-5.03470.16191600.1412827X-RAY DIFFRACTION98
5.0347-50.70730.19031680.17862860X-RAY DIFFRACTION97

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