+Open data
-Basic information
Entry | Database: PDB / ID: 2ivx | ||||||
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Title | Crystal structure of human cyclin T2 at 1.8 A resolution | ||||||
Components | CYCLIN-T2 | ||||||
Keywords | NUCLEAR PROTEIN / TRANSCRIPTION REGULATION / CELL DIVISION / PHOSPHORYLATION / CYCLIN / CELL CYCLE / TRANSCRIPTION | ||||||
Function / homology | Function and homology information early viral transcription / late viral transcription / 7SK snRNA binding / regulation of muscle cell differentiation / cyclin/CDK positive transcription elongation factor complex / snRNA transcription by RNA polymerase II / cyclin-dependent protein serine/threonine kinase activator activity / RNA polymerase binding / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA-templated transcription, elongation ...early viral transcription / late viral transcription / 7SK snRNA binding / regulation of muscle cell differentiation / cyclin/CDK positive transcription elongation factor complex / snRNA transcription by RNA polymerase II / cyclin-dependent protein serine/threonine kinase activator activity / RNA polymerase binding / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA-templated transcription, elongation / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / skeletal muscle tissue development / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / transcription coactivator binding / transcription by RNA polymerase II / cell cycle / cell division / host cell nucleus / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Debreczeni, J.E. / Bullock, A.N. / Fedorov, O. / Savitsky, P. / Berridge, G. / Das, S. / Pike, A.C.W. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. ...Debreczeni, J.E. / Bullock, A.N. / Fedorov, O. / Savitsky, P. / Berridge, G. / Das, S. / Pike, A.C.W. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. / Gorrec, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / von Delft, F. / Knapp, S. | ||||||
Citation | Journal: EMBO J. / Year: 2008 Title: The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation. Authors: Baumli, S. / Lolli, G. / Lowe, E.D. / Troiani, S. / Rusconi, L. / Bullock, A.N. / Debreczeni, J.E. / Knapp, S. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ivx.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ivx.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ivx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ivx ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ivx | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99991, -0.00938, -0.01004), Vector: |
-Components
#1: Protein | Mass: 29823.418 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-263 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: O60583 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 130 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 130 TO ARG ...ENGINEERED | |
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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: 2.79 Å3/Da / Density % sol: 55 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: 0.2M NA-FORMATE, 0.1M BIS-TRIS-PROPANE PH 8.5, 20%PEG3350, 10% ETHYLENE GLYCOL, 150 NL SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.86 Å / Num. obs: 53530 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.57 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.31 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.36 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→59.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.022 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→59.76 Å
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