+Open data
-Basic information
Entry | Database: PDB / ID: 6a73 | ||||||
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Title | Complex structure of CSN2 with IP6 | ||||||
Components | COP9 signalosome complex subunit 2,Endolysin | ||||||
Keywords | SIGNALING PROTEIN / subunit2 of COP9 Signalosome (CSN). | ||||||
Function / homology | Function and homology information trophectodermal cell proliferation / regulation of protein neddylation / protein deneddylation / COP9 signalosome / protein neddylation / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / skeletal muscle cell differentiation / viral release from host cell by cytolysis / peptidoglycan catabolic process ...trophectodermal cell proliferation / regulation of protein neddylation / protein deneddylation / COP9 signalosome / protein neddylation / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / skeletal muscle cell differentiation / viral release from host cell by cytolysis / peptidoglycan catabolic process / DNA Damage Recognition in GG-NER / neuron differentiation / Formation of TC-NER Pre-Incision Complex / transcription corepressor activity / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / transcription by RNA polymerase II / defense response to bacterium / protein phosphorylation / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage RB59 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.447 Å | ||||||
Authors | Liu, L. / Li, D. / Rao, F. / Wang, T. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome. Authors: Lin, H. / Zhang, X. / Liu, L. / Fu, Q. / Zang, C. / Ding, Y. / Su, Y. / Xu, Z. / He, S. / Yang, X. / Wei, X. / Mao, H. / Cui, Y. / Wei, Y. / Zhou, C. / Du, L. / Huang, N. / Zheng, N. / Wang, T. / Rao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a73.cif.gz | 261.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a73.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 6a73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a73 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a73 | HTTPS FTP |
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-Related structure data
-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: 35315.383 Da / Num. of mol.: 2 / Mutation: C54T, C97A Source method: isolated from a genetically manipulated source Details: human CSN2 hybrid with lysozyme,human CSN2 hybrid with lysozyme,human CSN2 hybrid with lysozyme,human CSN2 hybrid with lysozyme Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (virus) Gene: COPS2, CSN2, TRIP15, e, RB59_126 / Production host: Escherichia coli (E. coli) / References: UniProt: P61201, UniProt: A0A097J809, lysozyme #2: Chemical | #3: Chemical | #4: 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: 3.13 Å3/Da / Density % sol: 60.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate ,100mM Bis-Tris pH 5.5, 25%PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.447→20.003 Å / Num. obs: 27516 / % possible obs: 91.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.45→2.49 Å / Rmerge(I) obs: 0.189 / Num. unique obs: 1305 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L17 and 4ZWJ Resolution: 2.447→20.003 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.82 / Phase error: 34.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.447→20.003 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.3689 Å / Origin y: 7.5026 Å / Origin z: -57.8356 Å
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Refinement TLS group | Selection details: all |