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- PDB-5bnj: CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4... -

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Basic information

Entry
Database: PDB / ID: 5bnj
TitleCDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-phenyl]-pyridin- 4-yl}-2,8-diaza-spiro[4.5]decan-1-one
Components
  • Cyclin-C
  • Cyclin-dependent kinase 8
KeywordsTRANSFERASE / CDK8 KINASE / CYCLIN C / transferase
Function / homology
Function and homology information


PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Generic Transcription Pathway / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / [RNA-polymerase]-subunit kinase / mediator complex / cyclin-dependent protein serine/threonine kinase regulator activity ...PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Generic Transcription Pathway / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / [RNA-polymerase]-subunit kinase / mediator complex / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription initiation from RNA polymerase II promoter / protein kinase activity / regulation of transcription by RNA polymerase II / nucleolus / protein phosphorylation / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus
Cyclin-like / Protein kinase domain / Cyclin, C-terminal domain 2 / Cyclin C/cyclin-like subunit Ssn8 / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Cyclin, N-terminal / Protein kinase domain / Cyclin, N-terminal domain ...Cyclin-like / Protein kinase domain / Cyclin, C-terminal domain 2 / Cyclin C/cyclin-like subunit Ssn8 / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Cyclin, N-terminal / Protein kinase domain / Cyclin, N-terminal domain / Cyclin C-terminal domain / Cyclin-like superfamily / Protein kinases ATP-binding region signature. / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile.
Cyclin-C / Cyclin-dependent kinase 8
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsMusil, D. / Blagg, J. / Wienke, D.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease.
Authors: Dale, T. / Clarke, P.A. / Esdar, C. / Waalboer, D. / Adeniji-Popoola, O. / Ortiz-Ruiz, M.J. / Mallinger, A. / Samant, R.S. / Czodrowski, P. / Musil, D. / Schwarz, D. / Schneider, K. / Stubbs, M. / Ewan, K. / Fraser, E. / TePoele, R. / Court, W. / Box, G. / Valenti, M. / de Haven Brandon, A. / Gowan, S. / Rohdich, F. / Raynaud, F. / Schneider, R. / Poeschke, O. / Blaukat, A. / Workman, P. / Schiemann, K. / Eccles, S.A. / Wienke, D. / Blagg, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 26, 2015 / Release: Oct 14, 2015
RevisionDateData content typeGroupProviderType
1.0Oct 14, 2015Structure modelrepositoryInitial release
1.1Oct 21, 2015Structure modelDatabase references
1.2Oct 28, 2015Structure modelDatabase references
1.3Nov 11, 2015Structure modelDatabase references
1.4Nov 25, 2015Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,9855
Polymers80,4712
Non-polymers5143
Water1,02757
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-24 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)70.787, 71.489, 172.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Cyclin-dependent kinase 8 / / 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: KINASE DOMAIN, residues 3-405
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/peptide Cyclin-C / SRB11 homolog / hSRB11


Mass: 33479.953 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-4TV / 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one


Mass: 421.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClN5O
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Formic acid
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: 20% PEG3350, 0.2 M sodium formate, pH 6.9,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→86.27 Å / Num. obs: 25877 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.1
Reflection shellResolution: 2.64→2.89 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.523 / Rejects: 0 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMAC5.2.0005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.64→86.27 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.401 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.588 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 888 3.4 %RANDOM
Rwork0.2261 ---
Obs0.2277 24989 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.88 Å2 / Biso mean: 46.604 Å2 / Biso min: 28.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---3.14 Å20 Å2
3---3.97 Å2
Refinement stepCycle: final / Resolution: 2.64→86.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 36 57 5143
Biso mean--52.35 42.88 -
Num. residues----609
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0090.0225004
r_bond_other_d0.0020.024535
r_angle_refined_deg1.0821.9636800
r_angle_other_deg0.884310450
r_dihedral_angle_1_deg5.3985604
r_dihedral_angle_2_deg34.66823.425219
r_dihedral_angle_3_deg11.96415809
r_dihedral_angle_4_deg13.4241526
r_chiral_restr0.0610.2746
r_gen_planes_refined0.0030.025510
r_gen_planes_other0.0010.021054
r_nbd_refined0.1570.2932
r_nbd_other0.1230.24076
r_nbtor_refined0.1590.22407
r_nbtor_other0.0740.22482
r_xyhbond_nbd_refined0.0980.2104
r_symmetry_vdw_refined0.1060.27
r_symmetry_vdw_other0.1370.245
r_symmetry_hbond_refined0.0740.25
r_mcbond_it1.323971
r_mcbond_other0.16121214
r_mcangle_it1.49434901
r_scbond_it1.93842352
r_scangle_it2.94861899
LS refinement shellResolution: 2.64→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 57 -
Rwork0.36 1823 -
All-1880 -
Obs--98.43 %

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