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- PDB-2pk2: Cyclin box structure of the P-TEFb subunit Cyclin T1 derived from... -

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Basic information

Entry
Database: PDB / ID: 2pk2
TitleCyclin box structure of the P-TEFb subunit Cyclin T1 derived from a fusion complex with EIAV Tat
ComponentsCyclin-T1, Protein Tat
KeywordsCELL CYCLE / CYCLIN T1 / TAT / TAR / TWINNING / TRANSCRIPTION REGULATION P-TEFb
Function / homology
Function and homology information


P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / host cell nucleolus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation ...P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / host cell nucleolus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / regulation of cyclin-dependent protein serine/threonine kinase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA-binding transcription regulator activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / viral process / molecular condensate scaffold activity / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / transcription cis-regulatory region binding / response to xenobiotic stimulus / cell cycle / cell division / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like ...Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclin-T1 / Protein Tat
Similarity search - Component
Biological speciesHomo sapiens (human)
Equine infectious anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsAnand, K. / Schulte, A. / Fujinaga, K. / Scheffzek, K. / Geyer, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Cyclin Box Structure of the P-TEFb Subunit Cyclin T1 Derived from a Fusion Complex with EIAV Tat.
Authors: Anand, K. / Schulte, A. / Fujinaga, K. / Scheffzek, K. / Geyer, M.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL ASSEMBLY IS A TETRAMER, GENERATED FROM TWO DIMERS IN THE ASYMMETRIC UNIT BY TWIN OPERATIONS:1/3 2/3 2/3, -1/3 1/3 -2/3, -4/3 -2/3 1/3, 4. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999SEQUENCE Authors state the nucleotide sequence is GenBank entry AF048730 (human Cyclin T1), which ...SEQUENCE Authors state the nucleotide sequence is GenBank entry AF048730 (human Cyclin T1), which refers to the GenPept entry AAC39664. Residue 77 is Gln in UNP entry O60563, but is Arg in AF048730. Authors state the electron density map accommodates Arg side chain very well.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Cyclin-T1, Protein Tat
B: Cyclin-T1, Protein Tat
C: Cyclin-T1, Protein Tat
D: Cyclin-T1, Protein Tat


Theoretical massNumber of molelcules
Total (without water)161,3674
Polymers161,3674
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.830, 203.830, 124.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a tetramer, generated from two dimers in the asymmetric unit by twin operations:1/3 2/3 2/3, -1/3 1/3 -2/3, -4/3 -2/3 1/3, 4

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Components

#1: Protein
Cyclin-T1, Protein Tat / CycT1 / Cyclin-T / Transactivating regulatory protein / eQUINE Tat / E-Tat


Mass: 40341.637 Da / Num. of mol.: 4
Fragment: fusion protein of Cyclin T1 residues 1-281 and Protein EIAV Tat residues 19-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Equine infectious anemia virus
Genus: Homo, Lentivirus / Species: , / Strain: , / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60563, UniProt: P32544
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.9M Ammonium Sulfate, 5% Polyethylene Glycol 400 and 50 mM MES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2005 / Details: mirrors
RadiationMonochromator: Si(311) silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 55259 / Num. obs: 54763 / % possible obs: 99 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.06
Reflection shellHighest resolution: 2.67 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→50 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: The data is tetartohedral twinning with twinning operators: (h/3 2k/3 2l/3),(-h/3 k/3 -2l/3),(-4h/3 -2k/3 l/3) and corresponding twinned fractions: 0.187, 0.257, 0.178, 0.377.
RfactorNum. reflection
Rfree0.306 1547
Rwork0.274 -
all0.274 55259
obs0.272 54763
Refinement stepCycle: LAST / Resolution: 2.67→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8317 0 0 79 8396
LS refinement shellResolution: 2.67→2.7 Å

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