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- PDB-4un0: Crystal structure of the human CDK12-cyclinK complex -

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Basic information

Entry
Database: PDB / ID: 4un0
TitleCrystal structure of the human CDK12-cyclinK complex
Components
  • CYCLIN-DEPENDENT KINASE 12
  • CYCLIN-K
KeywordsTRANSFERASE
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of stem cell differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / host-mediated suppression of viral genome replication / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of stem cell differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cellular response to estrogen stimulus / regulation of signal transduction / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / negative regulation of MAPK cascade / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / cyclin binding / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / transcription by RNA polymerase II / protein kinase activity / nuclear speck / cell division / protein serine kinase activity / DNA damage response / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / 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/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cyclin-K / Cyclin-dependent kinase 12
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsDixon Clarke, S.E. / Elkins, J.M. / Pike, A.C.W. / Chaikuad, A. / Goubin, S. / Krojer, T. / Sorrell, F.J. / Nowak, R. / Williams, E. / Kopec, J. ...Dixon Clarke, S.E. / Elkins, J.M. / Pike, A.C.W. / Chaikuad, A. / Goubin, S. / Krojer, T. / Sorrell, F.J. / Nowak, R. / Williams, E. / Kopec, J. / Mahajan, R.P. / Burgess-Brown, N. / Carpenter, E.P. / Knapp, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Sci.Rep. / Year: 2015
Title: Structures of the Cdk12/Cyck Complex with AMP-Pnp Reveal a Flexible C-Terminal Kinase Extension Important for ATP Binding.
Authors: Dixon-Clarke, S.E. / Elkins, J.M. / Cheng, S.G. / Morin, G.B. / Bullock, A.N.
History
DepositionMay 22, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionJun 4, 2014ID: 4CJY
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-K
B: CYCLIN-K
C: CYCLIN-DEPENDENT KINASE 12
D: CYCLIN-DEPENDENT KINASE 12


Theoretical massNumber of molelcules
Total (without water)136,5264
Polymers136,5264
Non-polymers00
Water00
1
A: CYCLIN-K
C: CYCLIN-DEPENDENT KINASE 12


Theoretical massNumber of molelcules
Total (without water)68,2632
Polymers68,2632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-9 kcal/mol
Surface area24110 Å2
MethodPISA
2
B: CYCLIN-K
D: CYCLIN-DEPENDENT KINASE 12


Theoretical massNumber of molelcules
Total (without water)68,2632
Polymers68,2632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8.1 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.580, 148.780, 92.150
Angle α, β, γ (deg.)90.00, 94.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.49874, -0.48132, -0.72082), (-0.49815, -0.83974, 0.21605), (-0.70929, 0.25132, -0.65859)48.99984, -96.04948, 168.47206
2given(0.52625, -0.4852, -0.69831), (-0.49544, -0.84239, 0.21194), (-0.69108, 0.23444, -0.6837)46.46602, -95.12892, 171.76483

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Components

#1: Protein CYCLIN-K / CCNK


Mass: 30443.148 Da / Num. of mol.: 2 / Fragment: CYCLIN K, RESIDUES 11-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75909
#2: Protein CYCLIN-DEPENDENT KINASE 12 / CDC2-RELATED KINASE / ARGININE/SERINE-RICH / CRKRS / CELL DIVISION CYCLE 2-RELATED PROTEIN KINASE 7 ...CDC2-RELATED KINASE / ARGININE/SERINE-RICH / CRKRS / CELL DIVISION CYCLE 2-RELATED PROTEIN KINASE 7 / CDC2-RELATED PROTEIN KINASE 7 / CELL DIVISION PROTEIN KINASE 12 / HCDK12 / CDK12


Mass: 37819.672 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 715-1038
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NYV4, cyclin-dependent kinase
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE
Crystal growpH: 6.5
Details: 20% PEG3350, 10% ETGLY, 0.1M BISTRIS PROPANE PH6.5, 0.2M SODIUM NITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.15→57.82 Å / Num. obs: 22936 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 61.62 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.7
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2I53 AND 4BCG

2i53

4bcg


Resolution: 3.15→57.821 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 1188 5.2 %
Rwork0.2154 --
obs0.2172 22903 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→57.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8190 0 0 0 8190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028395
X-RAY DIFFRACTIONf_angle_d0.57911440
X-RAY DIFFRACTIONf_dihedral_angle_d10.792910
X-RAY DIFFRACTIONf_chiral_restr0.0241305
X-RAY DIFFRACTIONf_plane_restr0.0041445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.29340.35051690.32622702X-RAY DIFFRACTION99
3.2934-3.4670.31531360.27472688X-RAY DIFFRACTION99
3.467-3.68420.30851400.24722707X-RAY DIFFRACTION99
3.6842-3.96860.26211440.22692707X-RAY DIFFRACTION99
3.9686-4.36790.26941570.192705X-RAY DIFFRACTION99
4.3679-4.99960.23051470.18912737X-RAY DIFFRACTION99
4.9996-6.29770.29721480.21592728X-RAY DIFFRACTION100
6.2977-57.83060.22681470.17352741X-RAY DIFFRACTION99

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