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

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Basic information

Entry
Database: PDB / ID: 5mjy
TitleCrystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure)
Components
  • Tyrosine-protein phosphatase non-receptor type 23
  • Zinc finger FYVE domain-containing protein 9
KeywordsHYDROLASE / ESCRT-III SARA
Function / homology
Function and homology information


positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / 1-phosphatidylinositol binding / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / early endosome to late endosome transport ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / 1-phosphatidylinositol binding / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endocytic recycling / Interleukin-37 signaling / endosomal transport / TGF-beta receptor signaling activates SMADs / cilium assembly / dephosphorylation / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / protein-tyrosine-phosphatase / ciliary basal body / protein tyrosine phosphatase activity / endocytosis / early endosome membrane / nuclear body / early endosome / endosome / protein domain specific binding / intracellular membrane-bounded organelle / protein kinase binding / protein-containing complex / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like ...Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / 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 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / 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 / Zinc finger, FYVE/PHD-type / Alpha Horseshoe / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
Zinc finger FYVE domain-containing protein 9 / Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.2Jan 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

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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: Tyrosine-protein phosphatase non-receptor type 23
D: Tyrosine-protein phosphatase non-receptor type 23
E: Zinc finger FYVE domain-containing protein 9
F: Zinc finger FYVE domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)168,3046
Polymers168,3046
Non-polymers00
Water8,845491
1
A: Tyrosine-protein phosphatase non-receptor type 23
B: Tyrosine-protein phosphatase non-receptor type 23
F: Zinc finger FYVE domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)84,1523
Polymers84,1523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tyrosine-protein phosphatase non-receptor type 23
D: Tyrosine-protein phosphatase non-receptor type 23
E: Zinc finger FYVE domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)84,1523
Polymers84,1523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.330, 70.360, 83.480
Angle α, β, γ (deg.)111.48, 90.06, 93.00
Int Tables number1
Space group name H-MP1

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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.: 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 Zinc finger FYVE domain-containing protein 9 / / Mothers against decapentaplegic homolog-interacting protein / Madh-interacting protein / Novel ...Mothers against decapentaplegic homolog-interacting protein / Madh-interacting protein / Novel serine protease / NSP / Receptor activation anchor / hSARA / Smad anchor for receptor activation


Mass: 2711.885 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95405
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 42.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1 M MMT buffer pH 9.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.25→65.368 Å / Num. obs: 63820 / % possible obs: 95.85 % / Redundancy: 2.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.79
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.83 / CC1/2: 0.77 / % possible all: 93.75

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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: 2.25→65.368 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.2346 3008 4.71 %
Rwork0.1869 --
obs0.1892 63815 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→65.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11725 0 0 491 12216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211979
X-RAY DIFFRACTIONf_angle_d0.48716180
X-RAY DIFFRACTIONf_dihedral_angle_d13.1797310
X-RAY DIFFRACTIONf_chiral_restr0.0361754
X-RAY DIFFRACTIONf_plane_restr0.0032105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.28690.32911530.24132872X-RAY DIFFRACTION94
2.2869-2.32630.27081400.22832815X-RAY DIFFRACTION94
2.3263-2.36860.28621320.2172793X-RAY DIFFRACTION92
2.3686-2.41420.30391450.20582670X-RAY DIFFRACTION90
2.4142-2.46350.28031440.21352930X-RAY DIFFRACTION97
2.4635-2.5170.25611510.20182929X-RAY DIFFRACTION97
2.517-2.57560.26841650.19842904X-RAY DIFFRACTION97
2.5756-2.640.27251440.19762941X-RAY DIFFRACTION97
2.64-2.71140.25231400.19962940X-RAY DIFFRACTION98
2.7114-2.79120.24971380.19532971X-RAY DIFFRACTION97
2.7912-2.88130.24671200.20332981X-RAY DIFFRACTION97
2.8813-2.98420.27211310.21322901X-RAY DIFFRACTION97
2.9842-3.10370.2841480.20652943X-RAY DIFFRACTION97
3.1037-3.2450.25381520.19842939X-RAY DIFFRACTION98
3.245-3.4160.24611480.19232919X-RAY DIFFRACTION97
3.416-3.63010.22191390.18592934X-RAY DIFFRACTION96
3.6301-3.91030.22681620.16752908X-RAY DIFFRACTION97
3.9103-4.30370.18461650.15832890X-RAY DIFFRACTION97
4.3037-4.92630.18311230.15182911X-RAY DIFFRACTION96
4.9263-6.20590.21531350.18582858X-RAY DIFFRACTION94
6.2059-65.39560.16871330.16552858X-RAY DIFFRACTION94

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