+Open data
-Basic information
Entry | Database: PDB / ID: 4d10 | ||||||
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Title | Crystal structure of the COP9 signalosome | ||||||
Components | (COP9 SIGNALOSOME COMPLEX SUBUNIT ...) x 8 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation ...regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / trophectodermal cell proliferation / macrophage migration inhibitory factor binding / regulation of IRE1-mediated unfolded protein response / exosomal secretion / deNEDDylase activity / GTPase inhibitor activity / eukaryotic translation initiation factor 3 complex / regulation of protein neddylation / protein deneddylation / COP9 signalosome / metal-dependent deubiquitinase activity / activation of NF-kappaB-inducing kinase activity / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / RHOBTB1 GTPase cycle / inner cell mass cell proliferation / protein deubiquitination / skeletal muscle cell differentiation / regulation of JNK cascade / response to light stimulus / JNK cascade / translation initiation factor activity / post-translational protein modification / DNA Damage Recognition in GG-NER / neuron differentiation / Formation of TC-NER Pre-Incision Complex / transcription corepressor activity / metallopeptidase activity / positive regulation of DNA-binding transcription factor activity / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / cell junction / Neddylation / ubiquitin-dependent protein catabolic process / in utero embryonic development / transcription by RNA polymerase II / transcription coactivator activity / regulation of cell cycle / nuclear speck / translation / negative regulation of cell population proliferation / protein phosphorylation / chromatin / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 Å | ||||||
Authors | Bunker, R.D. / Lingaraju, G.M. / Thoma, N.H. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Crystal Structure of the Human Cop9 Signalosome Authors: Lingaraju, G.M. / Bunker, R.D. / Cavadini, S. / Hess, D. / Hassiepen, U. / Renatus, M. / Fischer, E.S. / Thoma, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d10.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4d10.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 4d10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d10 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d10 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-COP9 SIGNALOSOME COMPLEX SUBUNIT ... , 8 types, 16 molecules AIBJCKDLEMFNGOHP
#1: Protein | Mass: 54222.805 Da / Num. of mol.: 2 / Fragment: RESIDUES 52-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13098 #2: Protein | Mass: 51992.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P61201 #3: Protein | Mass: 47924.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UNS2 #4: Protein | Mass: 46651.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9BT78 #5: Protein | Mass: 37621.742 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases) #6: Protein | Mass: 36531.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q7L5N1 #7: Protein | Mass: 24649.197 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UBW8 #8: Protein | Mass: 23442.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q99627 |
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-Non-polymers , 1 types, 2 molecules
#9: Chemical |
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-Details
Sequence details | CHAINS A AND I MAPS TO UNIPROT Q13098 ISOFORM 4 |
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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: 3.49 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 5.4 Details: CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011 / Details: DYNAMICALLY BENDABLE MIRROR | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.8→52 Å / Num. obs: 86875 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3 | |||||||||||||||
Reflection shell | Resolution: 3.8→3.81 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 3.8→50.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 45.893 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 189.557 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→50.87 Å
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Refine LS restraints |
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