+Open data
-Basic information
Entry | Database: PDB / ID: 5lm1 | ||||||
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Title | Crystal Structure of HD-PTP phosphatase in complex with UBAP1 | ||||||
Components |
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Keywords | HYDROLASE / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Levy, C. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lm1.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lm1.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/5lm1 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/5lm1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Protein/peptide | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.53 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KSCN, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.55→2.64 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.51 / % possible all: 100 |
-Processing
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→44.82 Å
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Refine LS restraints |
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LS refinement shell |
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