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- PDB-6r3s: CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH COMPOUND 1 -

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Basic information

Entry
Database: PDB / ID: 6r3s
TitleCRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH COMPOUND 1
Components
  • Cyclin-C
  • Cyclin-dependent kinase 8
KeywordsCELL CYCLE / KINASE
Function / homology
Function and homology information


CKM complex / G0 to G1 transition / negative regulation of triglyceride metabolic process / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of Notch signaling pathway / RSV-host interactions / cyclin-dependent kinase ...CKM complex / G0 to G1 transition / negative regulation of triglyceride metabolic process / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of Notch signaling pathway / RSV-host interactions / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / ubiquitin ligase complex / RNA polymerase II CTD heptapeptide repeat kinase activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / ubiquitin protein ligase activity / protein kinase activity / protein ubiquitination / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Cyclin, C-terminal domain 2 / Cyclin 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 ...Cyclin, C-terminal domain 2 / Cyclin 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 / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
FORMIC ACID / Chem-JRE / Cyclin-C / Cyclin-dependent kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBoettcher, J.
CitationJournal: Mol.Cancer Ther. / Year: 2020
Title: Selective and Potent CDK8/19 Inhibitors Enhance NK-Cell Activity and Promote Tumor Surveillance.
Authors: Hofmann, M.H. / Mani, R. / Engelhardt, H. / Impagnatiello, M.A. / Carotta, S. / Kerenyi, M. / Lorenzo-Herrero, S. / Bottcher, J. / Scharn, D. / Arnhof, H. / Zoephel, A. / Schnitzer, R. / ...Authors: Hofmann, M.H. / Mani, R. / Engelhardt, H. / Impagnatiello, M.A. / Carotta, S. / Kerenyi, M. / Lorenzo-Herrero, S. / Bottcher, J. / Scharn, D. / Arnhof, H. / Zoephel, A. / Schnitzer, R. / Gerstberger, T. / Sanderson, M.P. / Rajgolikar, G. / Goswami, S. / Vasu, S. / Ettmayer, P. / Gonzalez, S. / Pearson, M. / McConnell, D.B. / Kraut, N. / Muthusamy, N. / Moll, J.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 8
B: Cyclin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3497
Polymers80,8162
Non-polymers5335
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-22 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.598, 71.120, 169.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cyclin-dependent kinase 8 / Cell division protein kinase 8 / Mediator complex subunit CDK8 / Mediator of RNA polymerase II ...Cell division protein kinase 8 / Mediator complex subunit CDK8 / Mediator of RNA polymerase II transcription subunit CDK8 / Protein kinase K35


Mass: 47105.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49336, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-C / SRB11 homolog / hSRB11


Mass: 33710.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24863

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Non-polymers , 4 types, 218 molecules

#3: Chemical ChemComp-JRE / 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide


Mass: 332.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17ClN4O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.19→84.89 Å / Num. obs: 43086 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.48
Reflection shellResolution: 2.19→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.444 / Num. unique obs: 11853 / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→84.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.263 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22679 1460 3.4 %RANDOM
Rwork0.20071 ---
obs0.20161 41621 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0 Å2
2---0.18 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.19→84.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 36 213 5330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195117
X-RAY DIFFRACTIONr_bond_other_d0.0010.024818
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9646945
X-RAY DIFFRACTIONr_angle_other_deg2.546311047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65823.696230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62515851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5211526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215712
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021194
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3662.5582466
X-RAY DIFFRACTIONr_mcbond_other2.3662.562467
X-RAY DIFFRACTIONr_mcangle_it3.6424.2813079
X-RAY DIFFRACTIONr_mcangle_other3.6434.2823080
X-RAY DIFFRACTIONr_scbond_it3.0312.8732651
X-RAY DIFFRACTIONr_scbond_other2.9832.8632645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5454.6983867
X-RAY DIFFRACTIONr_long_range_B_refined7.3711.8495924
X-RAY DIFFRACTIONr_long_range_B_other7.34611.7445877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 101 -
Rwork0.286 3034 -
obs--97.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0338-3.1804-0.44255.01040.69721.04120.25450.2263-0.0202-0.3883-0.27630.08510.012-0.1210.02180.3318-0.0279-0.01830.2640.04560.17341.43970.2358.144
21.74240.7467-0.02592.8747-0.07791.1549-0.01460.2132-0.0257-0.17810.03410.04990.0364-0.0564-0.01940.1670.0087-0.02510.1088-0.0020.00510.32440.47857.512
31.7962-0.44270.07841.4744-0.40172.52610.0313-0.07360.04630.0330.03510.0033-0.09240.0568-0.06650.1305-0.03450.04510.0791-0.01290.0816-3.63769.93987.122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 99
2X-RAY DIFFRACTION2A100 - 365
3X-RAY DIFFRACTION3B-3 - 266

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