+Open data
-Basic information
Entry | Database: PDB / ID: 8rd1 | ||||||
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Title | HUWE1 WWE domain in complex with compound 4 | ||||||
Components | E3 ubiquitin-protein ligase HUWE1 | ||||||
Keywords | LIGASE / WWE domain | ||||||
Function / homology | Function and homology information histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å | ||||||
Authors | Muenzker, L. / Zak, K.M. / Boettcher, J. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Commun Biol / Year: 2024 Title: A ligand discovery toolbox for the WWE domain family of human E3 ligases. Authors: Munzker, L. / Kimani, S.W. / Fowkes, M.M. / Dong, A. / Zheng, H. / Li, Y. / Dasovich, M. / Zak, K.M. / Leung, A.K.L. / Elkins, J.M. / Kessler, D. / Arrowsmith, C.H. / Halabelian, L. / Bottcher, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rd1.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rd1.ent.gz | 168.7 KB | Display | PDB format |
PDBx/mmJSON format | 8rd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rd1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8rd1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8rd1_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8rd1_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/8rd1 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/8rd1 | HTTPS FTP |
-Related structure data
Related structure data | 8r5nC 8r6aC 8r6bC 8r7oC 8rd0C 8rd7C 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
#1: Protein | Mass: 10519.563 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6Z7 #2: Chemical | ChemComp-CL / #3: Chemical | Mass: 249.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H7NO6 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / Details: 0.1 M Na Acetate pH 4.83, 2.9 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.896→60.58 Å / Num. obs: 38225 / % possible obs: 93.2 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Net I/av σ(I): 12.7 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.896→1.928 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 532 / CC1/2: 0.647 / % possible all: 30.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.896→25.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.123
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Displacement parameters | Biso mean: 32.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.896→25.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.93 Å
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