+Open data
-Basic information
Entry | Database: PDB / ID: 8k6q | ||||||
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Title | Crystal structure of HOIL-1L LTM domain | ||||||
Components | RanBP-type and C3HC4-type zinc finger-containing protein 1 | ||||||
Keywords | STRUCTURAL PROTEIN / HOIL-1L / LTM | ||||||
Function / homology | Function and homology information protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / protein sequestering activity ...protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / protein sequestering activity / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / defense response to bacterium / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Yan, Z. / Pan, L.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN. Authors: Zhang, Y. / Xu, X. / Wang, Y. / Wang, Y. / Zhou, X. / Pan, L. #1: Journal: To Be Published Title: Crystal structure of HOIL-1L LTM domain Authors: Yan, Z. / Pan, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k6q.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k6q.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 8k6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k6q_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 8k6q_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 8k6q_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 8k6q_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/8k6q ftp://data.pdbj.org/pub/pdb/validation_reports/k6/8k6q | HTTPS FTP |
-Related structure data
Related structure data | 8k6pC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6166.103 Da / Num. of mol.: 4 / Fragment: LTM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBCK1, C20orf18, RNF54, UBCE7IP3, XAP3, XAP4 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BYM8, RBR-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: 1.95 Å3/Da / Density % sol: 31.79 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium acetate, 1 M di-ammonium hydrogen phosphate (pH 4.5). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→44.4 Å / Num. obs: 21915 / % possible obs: 92.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 20.77 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.59→1.65 Å / Num. unique obs: 1379 / CC1/2: 0.879 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→44.4 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2254 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 28.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→44.4 Å
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Refine LS restraints |
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LS refinement shell |
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