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- PDB-4cxa: Crystal structure of the human CDK12-cyclin K complex bound to AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4cxa
TitleCrystal structure of the human CDK12-cyclin K complex bound to AMPPNP
Components
  • CYCLIN-DEPENDENT KINASE 12
  • CYCLIN-K
KeywordsTRANSFERASE / KINASE
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 / cyclin binding / RNA splicing / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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. / Nowak, R. / Goubin, S. / Mahajan, R.P. / Kopec, J. / Froese, S. / Tallant, C. / Carpenter, E.P. ...Dixon Clarke, S.E. / Elkins, J.M. / Pike, A.C.W. / Nowak, R. / Goubin, S. / Mahajan, R.P. / Kopec, J. / Froese, S. / Tallant, C. / Carpenter, E.P. / Mackenzie, A. / Faust, B. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / 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
DepositionApr 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,8325
Polymers140,3264
Non-polymers5061
Water00
1
C: CYCLIN-DEPENDENT KINASE 12
D: CYCLIN-K


Theoretical massNumber of molelcules
Total (without water)70,1632
Polymers70,1632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12.7 kcal/mol
Surface area25050 Å2
MethodPISA
2
A: CYCLIN-DEPENDENT KINASE 12
B: CYCLIN-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6693
Polymers70,1632
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-15.3 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.843, 138.791, 71.888
Angle α, β, γ (deg.)90.00, 104.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.243, 0.005, -0.97), (0.017, -1, -0.001), (-0.97, -0.016, -0.243)3.81661, -3.50484, 2.57516
2given(0.224, -0.007, -0.975), (-0.041, -0.999, -0.002), (-0.974, 0.041, -0.224)4.44955, -2.75327, 2.08356

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Components

#1: 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: 39719.922 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 715-1052
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NYV4, cyclin-dependent kinase
#2: 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 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75909
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: 2.22 Å3/Da / Density % sol: 48.72 % / Description: NONE
Crystal growpH: 7 / Details: 0.15M DL-MALIC ACID, 20% PEG3350, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97868
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97868 Å / Relative weight: 1
ReflectionResolution: 3.15→30.53 Å / Num. obs: 22908 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.4
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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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 ENTRY 4CJY

4cjy
PDB Unreleased entry


Resolution: 3.15→30.529 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 1069 4.7 %
Rwork0.2211 --
obs0.2239 22880 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→30.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8650 0 31 0 8681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048909
X-RAY DIFFRACTIONf_angle_d0.86812198
X-RAY DIFFRACTIONf_dihedral_angle_d13.1892994
X-RAY DIFFRACTIONf_chiral_restr0.0371399
X-RAY DIFFRACTIONf_plane_restr0.0041554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.29320.36771190.32442735X-RAY DIFFRACTION100
3.2932-3.46660.36831240.30342734X-RAY DIFFRACTION100
3.4666-3.68350.3471430.27382699X-RAY DIFFRACTION100
3.6835-3.96730.29981340.23342712X-RAY DIFFRACTION100
3.9673-4.36560.27251320.20672731X-RAY DIFFRACTION100
4.3656-4.99490.23831440.19432714X-RAY DIFFRACTION100
4.9949-6.2840.28561410.21392724X-RAY DIFFRACTION100
6.284-30.53010.22181320.17562762X-RAY DIFFRACTION100

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