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- PDB-3rgf: Crystal Structure of human CDK8/CycC -

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Basic information

Entry
Database: PDB / ID: 3rgf
TitleCrystal Structure of human CDK8/CycC
Components
  • Cyclin-C
  • Cyclin-dependent kinase 8
KeywordsTRANSFERASE / TRANSCRIPTION / protein kinase 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-BAX / 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. / Blaesse, M. / Huber, R. / Maskos, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Structure of CDK8/CycC Implicates Specificity in the CDK/Cyclin Family and Reveals Interaction with a Deep Pocket Binder.
Authors: Schneider, E.V. / Bottcher, J. / Blaesse, M. / Neumann, L. / Huber, R. / Maskos, K.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2Oct 3, 2012Group: Non-polymer description
Revision 1.3Sep 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)81,71015
Polymers80,4712
Non-polymers1,24013
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint3 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.690, 70.610, 79.140
Angle α, β, γ (deg.)90.000, 108.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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

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Non-polymers , 4 types, 188 molecules

#3: Chemical ChemComp-BAX / 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE / Sorafenib / Sorafenib


Mass: 464.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16ClF3N4O3 / Comment: inhibitor*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.2M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→37.567 Å / Num. obs: 37725 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.542 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH

1zp2

2i53

2pk2

2wh2
PDB Unreleased entry

2pk2

2rk3

2uze

2r3q

2r3n

2vth


Resolution: 2.2→37.567 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.809 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1885 5 %RANDOM
Rwork0.1805 ---
obs0.1826 37691 99.92 %-
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 max: 105.28 Å2 / Biso mean: 44.536 Å2 / Biso min: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.17 Å2
2--0.86 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 82 175 5126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224947
X-RAY DIFFRACTIONr_bond_other_d0.0010.023467
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9716680
X-RAY DIFFRACTIONr_angle_other_deg0.80238347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0185583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67923.333219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43115841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.941528
X-RAY DIFFRACTIONr_chiral_restr0.0610.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021041
X-RAY DIFFRACTIONr_mcbond_it1.34622938
X-RAY DIFFRACTIONr_mcbond_other0.33321162
X-RAY DIFFRACTIONr_mcangle_it2.39434733
X-RAY DIFFRACTIONr_scbond_it3.4942009
X-RAY DIFFRACTIONr_scangle_it5.32561947
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 139 -
Rwork0.22 2630 -
all-2769 -
obs--99.82 %
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)
14.8364-2.66010.42941.6029-0.44550.3951-0.1947-0.34440.02270.25020.17430.0353-0.2253-0.02710.02040.1582-0.04560.03780.2225-0.03110.1845-17.217.09926.642
22.85770.58860.07791.77890.10091.38170.0779-0.22170.07530.161-0.0182-0.0905-0.05970.0114-0.05970.0403-0.0101-0.00370.0338-0.00450.012214.199-2.29926.725
31.2113-0.2621-0.01991.6065-0.12572.60880.09-0.0038-0.0724-0.079-0.01480.07350.09870.055-0.07520.0228-0.0071-0.00910.01050.00230.043-16.35712.275-2.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2A101 - 353
3X-RAY DIFFRACTION3B1 - 264

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