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- PDB-4f7s: Crystal structure of human CDK8/CYCC in the DMG-in conformation -

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Basic information

Entry
Database: PDB / ID: 4f7s
TitleCrystal structure of human CDK8/CYCC in the DMG-in conformation
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 / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RSV-host interactions / negative regulation of Notch signaling pathway / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity ...CKM complex / G0 to G1 transition / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RSV-host interactions / negative regulation of Notch signaling pathway / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein kinase activity / 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 / : / 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
N-(2-phenylethyl)quinazolin-4-amine / FORMIC ACID / Cyclin-C / Cyclin-dependent kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)81,80317
Polymers80,7012
Non-polymers1,10215
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint17 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.498, 70.774, 170.141
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: 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

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Non-polymers , 4 types, 224 molecules

#3: Chemical ChemComp-0SW / N-(2-phenylethyl)quinazolin-4-amine


Mass: 249.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
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: 0.90001 / Wavelength: 0.90001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90001 Å / Relative weight: 1
ReflectionResolution: 2.2→85.07 Å / Num. all: 43856 / Num. obs: 43856 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.683 / % possible all: 99.5

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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: 2.2→85.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.88 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22193 1468 3.3 %RANDOM
Rwork0.19255 ---
all0.19354 43856 --
obs0.19354 42388 99.51 %-
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: 49.419 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.77 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→85.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 74 209 5306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225041
X-RAY DIFFRACTIONr_bond_other_d0.0020.023547
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9666810
X-RAY DIFFRACTIONr_angle_other_deg1.02138506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13523.198222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52915826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8951529
X-RAY DIFFRACTIONr_chiral_restr0.070.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215503
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021070
X-RAY DIFFRACTIONr_mcbond_it1.45323034
X-RAY DIFFRACTIONr_mcbond_other0.37321201
X-RAY DIFFRACTIONr_mcangle_it2.5534875
X-RAY DIFFRACTIONr_scbond_it3.71342007
X-RAY DIFFRACTIONr_scangle_it5.51961934
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 98 -
Rwork0.283 3073 -
obs--99.03 %
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)
11.4235-2.3074-0.54774.38310.56820.58910.17350.25560.0013-0.47-0.18370.197-0.0698-0.16520.01030.2599-0.0381-0.06210.19040.05750.17061.32569.90758.91
22.1070.6108-0.12162.97830.03411.21120.0040.2491-0.018-0.23190.03020.0670.0209-0.0318-0.03410.06810.0137-0.02290.09250.00280.009810.52640.36157.809
31.7838-0.4008-0.15391.2758-0.0362.28350.0197-0.08320.0942-0.01890.0469-0.0154-0.07190.0468-0.06660.0379-0.02390.01820.0439-0.00170.0817-3.44569.79387.44
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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