+Open data
-Basic information
Entry | Database: PDB / ID: 2vhf | ||||||
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Title | Structure of the CYLD USP domain | ||||||
Components | UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD | ||||||
Keywords | HYDROLASE / CYTOKINE SIGNALLING / LINKAGE SPECIFICITY / DEUBIQUITINATING ENZYME / LYS63- LINKED / ANTI-ONCOGENE / THIOL PROTEASE / CELL SIGNALLING / PHOSPHORYLATION / ZN-BINDING DOMAIN / UBIQUITIN / CELL CYCLE / USP DOMAIN / CROSS-BRACE / NF-KB / B-BOX / PROTEASE / CYTOPLASM / ALTERNATIVE SPLICING / UBL CONJUGATION PATHWAY | ||||||
Function / homology | Function and homology information negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / : / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip ...negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / : / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip / regulation of necroptotic process / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of JNK cascade / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / proline-rich region binding / negative regulation of non-canonical NF-kappaB signal transduction / K48-linked deubiquitinase activity / TNFR1-induced proapoptotic signaling / positive regulation of T cell differentiation / negative regulation of type I interferon production / K63-linked deubiquitinase activity / positive regulation of protein localization / positive regulation of T cell receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / necroptotic process / homeostasis of number of cells / regulation of microtubule cytoskeleton organization / regulation of mitotic cell cycle / ciliary basal body / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / spindle / negative regulation of inflammatory response / Wnt signaling pathway / regulation of inflammatory response / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / microtubule / Ub-specific processing proteases / cell cycle / innate immune response / centrosome / protein kinase binding / perinuclear region of cytoplasm / proteolysis / zinc ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Komander, D. / Lord, C.J. / Scheel, H. / Swift, S. / Hofmann, K. / Ashworth, A. / Barford, D. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2008 Title: The Structure of the Cyld Usp Domain Explains its Specificity for Lys63-Linked Polyubiquitin and Reveals a B-Box Module Authors: Komander, D. / Lord, C.J. / Scheel, H. / Swift, S. / Hofmann, K. / Ashworth, A. / Barford, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vhf.cif.gz | 272.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vhf.ent.gz | 228.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/2vhf ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vhf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43345.180 Da / Num. of mol.: 2 / Fragment: USP DEUBIQUITINASE DOMAIN, RESIDUES 583-956 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NQC7, EC: 3.1.2.15 #2: Chemical | ChemComp-ZN / #3: 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: 2.7 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 1.5-2% PEG 20000, 0.1 M MES [PH6.3], pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 23405 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.8→29.79 Å / SU ML: 0.53 / Cross valid method: PHENIX DEFAULT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFINED WITH PHENIX 1.3B DISORDERED SIDECHAINS WERE REFINED WITH OCCU 0.01 OR MUTATED TO ALA. ANISO RECORDS ARE CREATED BY TLS REFINEMENT IN PHENIX
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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: 58.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.79 Å
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