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- PDB-5mk1: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -

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Basic information

Entry
Database: PDB / ID: 5mk1
TitleCrystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure)
Components
  • Charged multivesicular body protein 4a
  • Tyrosine-protein phosphatase non-receptor type 23
KeywordsHYDROLASE / ESCRT-III CHMP4A
Function / homology
Function and homology information


positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / membrane invagination / plasma membrane tubulation / 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 ...positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / membrane invagination / plasma membrane tubulation / 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 / membrane coat / post-translational protein targeting to endoplasmic reticulum membrane / 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 / nervous system process / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / protein polymerization / 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 / ATPase binding / 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 / lipid binding / protein kinase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / 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 4a / Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLevy, C. / Gahloth, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K011049/1 United Kingdom
Medical Research Council (United Kingdom)G0701140 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

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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: Charged multivesicular body protein 4a
F: Charged multivesicular body protein 4a
H: Charged multivesicular body protein 4a
K: Charged multivesicular body protein 4a


Theoretical massNumber of molelcules
Total (without water)171,2338
Polymers171,2338
Non-polymers00
Water3,009167
1
A: Tyrosine-protein phosphatase non-receptor type 23
E: Charged multivesicular body protein 4a


Theoretical massNumber of molelcules
Total (without water)42,8082
Polymers42,8082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-9 kcal/mol
Surface area16980 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 23
F: Charged multivesicular body protein 4a


Theoretical massNumber of molelcules
Total (without water)42,8082
Polymers42,8082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area16890 Å2
MethodPISA
3
C: Tyrosine-protein phosphatase non-receptor type 23
H: Charged multivesicular body protein 4a


Theoretical massNumber of molelcules
Total (without water)42,8082
Polymers42,8082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-10 kcal/mol
Surface area17040 Å2
MethodPISA
4
D: Tyrosine-protein phosphatase non-receptor type 23
K: Charged multivesicular body protein 4a


Theoretical massNumber of molelcules
Total (without water)42,8082
Polymers42,8082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.458, 73.669, 79.383
Angle α, β, γ (deg.)114.43, 90.28, 104.20
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
Charged multivesicular body protein 4a / Chromatin-modifying protein 4a / CHMP4a / SNF7 homolog associated with Alix-2 / SNF7-1 / hSnf-1 / ...Chromatin-modifying protein 4a / CHMP4a / SNF7 homolog associated with Alix-2 / SNF7-1 / hSnf-1 / Vacuolar protein sorting-associated protein 32-1 / hVps32-1


Mass: 2088.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BY43
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350

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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: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→28.41 Å / Num. obs: 47548 / % possible obs: 93.05 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1342 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.94 / CC1/2: 0.442 / % possible all: 84.76

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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: 2.5→28.41 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2263 1770 3.87 %
Rwork0.1759 --
obs0.1779 45702 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11723 0 0 167 11890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711974
X-RAY DIFFRACTIONf_angle_d1.23216173
X-RAY DIFFRACTIONf_dihedral_angle_d7.9037305
X-RAY DIFFRACTIONf_chiral_restr0.061764
X-RAY DIFFRACTIONf_plane_restr0.0062092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56760.34431240.26243086X-RAY DIFFRACTION85
2.5676-2.64310.32271240.2423153X-RAY DIFFRACTION87
2.6431-2.72840.28881370.23813170X-RAY DIFFRACTION87
2.7284-2.82580.31221290.22693259X-RAY DIFFRACTION90
2.8258-2.93880.33061400.21153340X-RAY DIFFRACTION92
2.9388-3.07240.24991330.2073402X-RAY DIFFRACTION93
3.0724-3.23420.28871330.20243406X-RAY DIFFRACTION95
3.2342-3.43660.2361430.18473514X-RAY DIFFRACTION96
3.4366-3.70140.2341410.17063517X-RAY DIFFRACTION97
3.7014-4.0730.18191410.15123542X-RAY DIFFRACTION98
4.073-4.66020.18071410.13423527X-RAY DIFFRACTION97
4.6602-5.86340.18271420.16053508X-RAY DIFFRACTION97
5.8634-28.410.17961420.14943508X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73870.402-0.86680.7066-1.24882.8130.001-0.1347-0.0356-0.0332-0.0429-0.00520.04520.14690.05450.2801-0.002-0.00740.2596-0.03740.3121-3.184412.663414.3322
21.26040.3795-0.68430.5425-1.04133.1972-0.03510.00190.0649-0.0142-0.0252-0.00420.0037-0.06290.06170.24060.0170.00580.243-0.03380.288-37.103619.3357-0.2529
30.6873-0.37760.83840.7523-1.31393.27290.01630.07890.0246-0.0292-0.0207-0.02490.01830.0681-0.01390.26890.00610.010.2223-0.03810.2692-0.3772-10.2485-12.8741
40.903-0.23591.04350.4727-0.95433.3851-0.0558-0.092-0.08770.00930.07090.0445-0.0784-0.18750.01270.26770.00830.00530.2541-0.02090.3333-34.3835-17.35141.4389
55.8421.5158-0.04215.81374.32096.8088-0.0030.3865-0.3271-0.2595-0.0507-1.51510.47131.4751-0.10320.51330.04990.020.599-0.03610.72299.012-1.908621.205
66.8339-1.8142.52294.18190.67042.2710.1430.1010.04540.361-0.06961.36090.4262-1.32890.10790.4763-0.09520.05350.7617-0.17220.7083-49.322814.5944-16.249
78.33990.15620.3753.26291.02351.15150.3891-0.7572-0.41390.23090.0833-0.9072-0.36940.929-0.35180.78360.0513-0.05420.7394-0.06641.030612.11873.6372-19.9429
86.81721.7427-0.24130.82970.07420.29490.09960.15020.07170.0843-0.33030.5529-0.1102-0.80130.27350.46620.0301-0.03240.8694-0.06490.7962-46.4546-11.753516.9397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 361)
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 361)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 361)
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 361)
5X-RAY DIFFRACTION5(chain 'E' and resid 8 through 18)
6X-RAY DIFFRACTION6(chain 'F' and resid 8 through 18)
7X-RAY DIFFRACTION7(chain 'H' and resid 8 through 18)
8X-RAY DIFFRACTION8(chain 'K' and resid 8 through 18)

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