+Open data
-Basic information
Entry | Database: PDB / ID: 3rgf | ||||||
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Title | Crystal Structure of human CDK8/CycC | ||||||
Components |
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Keywords | TRANSFERASE / TRANSCRIPTION / protein kinase complex | ||||||
Function / homology | Function and homology information CKM complex / G0 to G1 transition / negative regulation of triglyceride metabolic process / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RSV-host interactions / negative regulation of Notch signaling pathway / cyclin-dependent kinase ...CKM complex / G0 to G1 transition / negative regulation of triglyceride metabolic process / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RSV-host interactions / negative regulation of Notch signaling pathway / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / ubiquitin ligase complex / RNA polymerase II CTD heptapeptide repeat kinase activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / ubiquitin protein ligase activity / protein kinase activity / protein ubiquitination / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schneider, E.V. / Boettcher, J. / Blaesse, M. / Huber, R. / Maskos, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Structure of CDK8/CycC Implicates Specificity in the CDK/Cyclin Family and Reveals Interaction with a Deep Pocket Binder. Authors: Schneider, E.V. / Bottcher, J. / Blaesse, M. / Neumann, L. / Huber, R. / Maskos, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rgf.cif.gz | 263.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rgf.ent.gz | 209.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/3rgf ftp://data.pdbj.org/pub/pdb/validation_reports/rg/3rgf | HTTPS FTP |
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-Related structure data
Related structure data | 1zp2S 2i53S 2pk2S 2r3nS 2r3qS 2rk3S 2uzeS 2vthS 2wh2 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 46990.801 Da / Num. of mol.: 1 / Fragment: UNP residues 1-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK8 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P49336, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 33479.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24863 |
-Non-polymers , 4 types, 188 molecules
#3: Chemical | ChemComp-BAX / | ||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG3350, 0.2M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.567 Å / Num. obs: 37725 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.542 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH Resolution: 2.2→37.567 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.809 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.28 Å2 / Biso mean: 44.536 Å2 / Biso min: 10.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→37.567 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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