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Yorodumi- PDB-8ei8: Crystal structure of the WWP2 HECT domain in complex with H308, a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ei8 | ||||||
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Title | Crystal structure of the WWP2 HECT domain in complex with H308, a Helicon Polypeptide | ||||||
Components |
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Keywords | LIGASE / E3 ligase / complex / stapled peptide | ||||||
Function / homology | Function and homology information negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination ...negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination / transcription factor binding / RHOU GTPase cycle / protein autoubiquitination / ubiquitin ligase complex / NOTCH3 Activation and Transmission of Signal to the Nucleus / regulation of membrane potential / protein modification process / negative regulation of DNA-binding transcription factor activity / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein ubiquitination / symbiont entry into host cell / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Li, K. / Tokareva, O.S. / Thomson, T.M. / Verdine, G.L. / McGee, J.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides. Authors: Tokareva, O.S. / Li, K. / Travaline, T.L. / Thomson, T.M. / Swiecicki, J.M. / Moussa, M. / Ramirez, J.D. / Litchman, S. / Verdine, G.L. / McGee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ei8.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ei8.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ei8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ei8_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 8ei8_full_validation.pdf.gz | 484.6 KB | Display | |
Data in XML | 8ei8_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 8ei8_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/8ei8 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/8ei8 | HTTPS FTP |
-Related structure data
Related structure data | 8ehzC 8ei0C 8ei1C 8ei2C 8ei3C 8ei4C 8ei5C 8ei6C 8ei7C 8ei9C 8eiaC 8eibC 8eicC 4y07S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 44925.391 Da / Num. of mol.: 1 / Fragment: HECT domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WWP2 / Production host: Escherichia coli (E. coli) References: UniProt: O00308, HECT-type E3 ubiquitin transferase |
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#2: Protein/peptide | Mass: 2073.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 6 molecules
#3: Chemical | ChemComp-PG4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-WHL / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris pH 6.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→43.77 Å / Num. obs: 9862 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.248 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1564 / CC1/2: 0.814 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y07 Resolution: 2.9→43.77 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.28 Å2 / Biso mean: 61.1609 Å2 / Biso min: 27.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→43.77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -22.7921 Å / Origin y: -26.6122 Å / Origin z: 10.9467 Å
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Refinement TLS group |
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