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- PDB-2i53: Crystal structure of Cyclin K -

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Basic information

Entry
Database: PDB / ID: 2i53
TitleCrystal structure of Cyclin K
ComponentsCyclin K
KeywordsCELL CYCLE / TRANSCRIPTION / CYCLIN K / CYCLIN BOX / CDK9 / POSITIVE TRANSCRIPTION ELONGATION FACTOR / P-TEFB
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / regulation of cyclin-dependent protein serine/threonine kinase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / regulation of cyclin-dependent protein serine/threonine kinase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / regulation of signal transduction / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / transcription by RNA polymerase II / cell cycle / cell division / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / nucleoplasm / nucleus
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Cyclin, C-terminal domain / Cyclin_C / 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-T2-like, C-terminal domain / Cyclin, C-terminal domain / Cyclin_C / 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
ACETATE ION / Cyclin-K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsBaek, K. / Brown, R.S. / Birrane, G. / Ladias, J.A.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Human Cyclin K, a Positive Regulator of Cyclin-dependent Kinase 9.
Authors: Baek, K. / Brown, R.S. / Birrane, G. / Ladias, J.A.
History
DepositionAug 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4594
Polymers30,2821
Non-polymers1773
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.766, 69.186, 50.504
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclin K


Mass: 30281.930 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 11-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O75909
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium sulfate, PEG 400, HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2005 / Details: MONOCHROMATOR
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 46197 / Num. obs: 46197 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 32.28
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→23.69 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.221 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2338 5.2 %RANDOM
Rwork0.183 ---
obs0.185 42446 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 228 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222176
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9492942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75423.925107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27615386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4911512
X-RAY DIFFRACTIONr_chiral_restr0.1290.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021659
X-RAY DIFFRACTIONr_nbd_refined0.2830.31163
X-RAY DIFFRACTIONr_nbtor_refined0.3250.51524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.5341
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.356
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.520
X-RAY DIFFRACTIONr_mcbond_it2.88421314
X-RAY DIFFRACTIONr_mcangle_it4.03332062
X-RAY DIFFRACTIONr_scbond_it5.6784996
X-RAY DIFFRACTIONr_scangle_it8.3466880
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 183 -
Rwork0.223 3083 -
obs--99.57 %

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