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- PDB-4g6l: Crystal structure of human CDK8/CYCC in the DMG-in conformation -

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Basic information

Entry
Database: PDB / ID: 4g6l
TitleCrystal structure of human CDK8/CYCC in the DMG-in conformation
Components
  • Cyclin-C
  • Cyclin-dependent kinase 8
KeywordsTRANSFERASE/TRANSCRIPTION / protein kinase complex / Proteros / TRANSFERASE-TRANSCRIPTION 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 / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / 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
FORMIC ACID / Cyclin-C / Cyclin-dependent kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchneider, E.V. / Blaesse, M. / 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
DepositionJul 19, 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)80,7473
Polymers80,7012
Non-polymers461
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-27 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.181, 70.942, 170.417
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: 47105.887 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: 33595.039 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-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 40 / 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: 53.2 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→85.21 Å / Num. all: 24071 / Num. obs: 24071 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 15.62
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 3.54 / Rsym value: 0.679 / % possible all: 99.7

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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: 2.7→85.21 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 23.944 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26625 844 3.5 %RANDOM
Rwork0.21179 ---
all0.21374 24071 --
obs0.21374 23226 --
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: 51.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---2.79 Å20 Å2
3---3.07 Å2
Refinement stepCycle: LAST / Resolution: 2.7→85.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 3 40 5047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224926
X-RAY DIFFRACTIONr_bond_other_d0.0020.023400
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9576675
X-RAY DIFFRACTIONr_angle_other_deg1.40238174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20923.333222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32915810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4511528
X-RAY DIFFRACTIONr_chiral_restr0.070.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021052
X-RAY DIFFRACTIONr_mcbond_it1.53523004
X-RAY DIFFRACTIONr_mcbond_other0.21221195
X-RAY DIFFRACTIONr_mcangle_it2.76234812
X-RAY DIFFRACTIONr_scbond_it3.85541922
X-RAY DIFFRACTIONr_scangle_it5.67261863
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 54 -
Rwork0.287 1670 -
obs--99.54 %
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)
12.04-3.1465-0.48055.01070.97051.84690.40680.36840.0256-0.6733-0.45860.1114-0.1416-0.23620.05180.3149-0.0243-0.00990.28330.05930.27671.38234.6228.862
22.39591.1679-0.02533.8374-0.20141.2839-0.00970.2504-0.0093-0.35720.02180.10120.0195-0.1312-0.01210.14990.0196-0.03080.15790.00240.007410.4824.553228.047
31.9749-0.49080.29131.7026-0.29693.33750.0542-0.07830.02140.0050.05730.0042-0.05110.016-0.11150.071-0.03990.03890.0618-0.00440.1046-3.73234.48257.957
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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