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- PDB-5lm1: Crystal Structure of HD-PTP phosphatase in complex with UBAP1 -

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Basic information

Entry
Database: PDB / ID: 5lm1
TitleCrystal Structure of HD-PTP phosphatase in complex with UBAP1
Components
  • Tyrosine-protein phosphatase non-receptor type 23
  • UBAP-1
KeywordsHYDROLASE / coiled coil
Function / homology
Function and homology information


positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / ESCRT I complex / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / 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 / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / ESCRT I complex / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / 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 / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endocytic recycling / Interleukin-37 signaling / cilium assembly / dephosphorylation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / protein-tyrosine-phosphatase / ciliary basal body / HCMV Late Events / ubiquitin binding / protein tyrosine phosphatase activity / Late endosomal microautophagy / Budding and maturation of HIV virion / nuclear body / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / protein kinase binding / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-associated protein 1 / Ubiquitin-associated protein 1, C-terminal / Ubiquitin-associated protein 1, UBA2 domain / UMA domain / UMA domain profile. / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain ...Ubiquitin-associated protein 1 / Ubiquitin-associated protein 1, C-terminal / Ubiquitin-associated protein 1, UBA2 domain / UMA domain / UMA domain profile. / 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 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 23 / Ubiquitin-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLevy, C.
CitationJournal: Structure / Year: 2016
Title: Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1.
Authors: Gahloth, D. / Levy, C. / Heaven, G. / Stefani, F. / Wunderley, L. / Mould, P. / Cliff, M.J. / Bella, J. / Fielding, A.J. / Woodman, P. / Tabernero, L.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references

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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: UBAP-1


Theoretical massNumber of molelcules
Total (without water)42,3902
Polymers42,3902
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-12 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.930, 93.270, 102.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 40162.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase
#2: Protein/peptide UBAP-1


Mass: 2227.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NZ09*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KSCN, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→44.82 Å / Num. obs: 15835 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.55
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.51 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE

Resolution: 2.55→44.82 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 31.56
RfactorNum. reflection% reflection
Rfree0.2539 783 4.95 %
Rwork0.213 --
obs0.2151 15833 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 0 31 2736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022741
X-RAY DIFFRACTIONf_angle_d0.3973701
X-RAY DIFFRACTIONf_dihedral_angle_d14.5651726
X-RAY DIFFRACTIONf_chiral_restr0.029435
X-RAY DIFFRACTIONf_plane_restr0.003482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.70980.39071080.31192484X-RAY DIFFRACTION100
2.7098-2.9190.33361220.27162469X-RAY DIFFRACTION100
2.919-3.21270.31631530.24132447X-RAY DIFFRACTION100
3.2127-3.67740.2691390.22352478X-RAY DIFFRACTION100
3.6774-4.63240.19841270.18932516X-RAY DIFFRACTION100
4.6324-44.82850.2391340.19392656X-RAY DIFFRACTION100

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