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- PDB-4f7l: Crystal structure of human CDK8/CYCC in complex with compound 2 (... -

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Basic information

Entry
Database: PDB / ID: 4f7l
TitleCrystal structure of human CDK8/CYCC in complex with compound 2 (tert-butyl [3-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)propyl]carbamate)
Components
  • Cyclin-C
  • Cyclin-dependent kinase 8
KeywordsTRANSFERASE/TRANSCRIPTION/INHIBITOR / protein kinase complex / Proteros / TRANSFERASE-TRANSCRIPTION-INHIBITOR complex
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 / cyclin-dependent protein kinase holoenzyme complex / 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 / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / 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 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / ubiquitin protein ligase activity / protein ubiquitination / protein kinase activity / phosphorylation / 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
Chem-0SO / Cyclin-C / Cyclin-dependent kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchneider, E.V. / Boettcher, J. / Huber, R. / Maskos, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-kinetic relationship study of CDK8/CycC specific compounds.
Authors: Schneider, E.V. / Bottcher, J. / Huber, R. / Maskos, K. / Neumann, L.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-dependent kinase 8
B: Cyclin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1303
Polymers80,7012
Non-polymers4301
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-27 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.819, 71.242, 171.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: 46990.801 Da / Num. of mol.: 1 / Fragment: UNP residues 1-403
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
#3: Chemical ChemComp-0SO / tert-butyl [3-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)propyl]carbamate


Mass: 429.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H35N5O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 / Wavelength: 0.99986 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.9→85.85 Å / Num. all: 19174 / Num. obs: 19174 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.9→3.09 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.432 / % possible all: 84.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RGF

3rgf


Resolution: 2.9→85.85 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.867 / SU B: 41.873 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26998 662 3.5 %RANDOM
Rwork0.2239 ---
all0.2255 19174 --
obs0.2255 18512 94.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.57 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→85.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 31 25 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224903
X-RAY DIFFRACTIONr_bond_other_d0.0020.023374
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9656658
X-RAY DIFFRACTIONr_angle_other_deg1.02138122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93923.727220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21115808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2761524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215397
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021023
X-RAY DIFFRACTIONr_mcbond_it1.48722970
X-RAY DIFFRACTIONr_mcbond_other0.27221177
X-RAY DIFFRACTIONr_mcangle_it2.70734769
X-RAY DIFFRACTIONr_scbond_it3.62741933
X-RAY DIFFRACTIONr_scangle_it5.70961889
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 55 -
Rwork0.379 1154 -
obs--81.36 %
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)
12.8948-2.75280.11094.6273-0.19930.81510.21290.43270.238-0.6424-0.1654-0.0537-0.1788-0.1608-0.04750.2774-0.06590.02770.20270.01570.128736.94969.884144.738
21.75740.98910.04134.032-0.51531.8457-0.02710.2559-0.1299-0.31050.0683-0.01060.0876-0.0975-0.04120.06690.01010.00960.0928-0.02420.017846.92539.646143.566
31.9632-0.2795-0.040.9165-0.12452.87280.0271-0.11770.1740.00730.0526-0.0423-0.007-0.0238-0.07980.0592-0.03150.02630.0322-0.01840.074131.57370.236174.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2A101 - 359
3X-RAY DIFFRACTION3B1 - 264

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