+Open data
-Basic information
Entry | Database: PDB / ID: 6qlz | ||||||
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Title | IDOL F3ab subdomain | ||||||
Components | E3 ubiquitin-protein ligase MYLIP | ||||||
Keywords | LIGASE / E3 LIGASE CHOLESTEROL METABOLISM LDLR degradation | ||||||
Function / homology | Function and homology information regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle clearance / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of protein catabolic process / ubiquitin-protein transferase activity ...regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle clearance / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of neuron projection development / nervous system development / ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.343 Å | ||||||
Authors | Martinelli, L. / Johansson, P. / Wan, P.T. / Gunnarsson, J. / Guo, H. / Boyd, H. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate-binding site. Authors: Martinelli, L. / Adamopoulos, A. / Johansson, P. / Wan, P.T. / Gunnarsson, J. / Guo, H. / Boyd, H. / Zelcer, N. / Sixma, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qlz.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qlz.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qlz_validation.pdf.gz | 408.7 KB | Display | wwPDB validaton report |
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Full document | 6qlz_full_validation.pdf.gz | 408.9 KB | Display | |
Data in XML | 6qlz_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 6qlz_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/6qlz ftp://data.pdbj.org/pub/pdb/validation_reports/ql/6qlz | HTTPS FTP |
-Related structure data
Related structure data | 6qlyC 2he7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11129.610 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYLIP, BZF1, IDOL, BM-023, PP5242 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T1R References: UniProt: Q8WY64, RING-type E3 ubiquitin transferase #2: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM Hepes pH 7.0 10% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.343→74.318 Å / Num. obs: 12704 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.108 / Rsym value: 0.084 / Net I/av σ(I): 7.7 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HE7 Resolution: 2.343→50 Å / Cross valid method: THROUGHOUT /
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Displacement parameters | Biso max: 141.86 Å2 / Biso mean: 63.5 Å2 / Biso min: 31.11 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.343→50 Å
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