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- PDB-4crl: Crystal structure of human CDK8-Cyclin C in complex with cortistatin A -

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Basic information

Entry
Database: PDB / ID: 4crl
TitleCrystal structure of human CDK8-Cyclin C in complex with cortistatin A
Components
  • CYCLIN-C
  • CYCLIN-DEPENDENT KINASE 8
KeywordsTRANSFERASE / CYCLIN-DEPENDENT KINASE 8 / CDK8 / CYCLIN C / CCNC / CORTISTATIN A / MEDIATOR KINASE / MEDIATOR COMPLEX / SUPER-ENHANCER / TRANSCRIPTION
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
CORTISTATIN A / FORMIC ACID / Cyclin-C / Cyclin-dependent kinase 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMyers, A.G. / Shair, M.D.
CitationJournal: Nature / Year: 2015
Title: Mediator Kinase Inhibition Further Activates Super-Enhancer- Associated Genes in Aml
Authors: Pelish, H.E. / Liau, B.B. / Nitulescu, I.I. / Tangpeerachaikul, A. / Poss, Z.C. / Da Silva, D.H. / Caruso, B.T. / Arefolov, A. / Fadeyi, O. / Christie, A.L. / Du, K. / Banka, D. / Schneider, ...Authors: Pelish, H.E. / Liau, B.B. / Nitulescu, I.I. / Tangpeerachaikul, A. / Poss, Z.C. / Da Silva, D.H. / Caruso, B.T. / Arefolov, A. / Fadeyi, O. / Christie, A.L. / Du, K. / Banka, D. / Schneider, E.V. / Jestel, A. / Zou, G. / Si, C. / Ebmeier, C.C. / Bronson, R.T. / Krivtsov, A.V. / Myers, A.G. / Kohl, N.E. / Kung, A.L. / Armstrong, S.A. / Lemieux, M.E. / Taatjes, D.J. / Shair, M.D.
History
DepositionFeb 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Jan 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)81,2898
Polymers80,5862
Non-polymers7036
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-25.5 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.490, 71.252, 171.247
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 / CDK8


Mass: 47105.887 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P49336, cyclin-dependent kinase
#2: Protein CYCLIN-C / SRB11 HOMOLOG / HSRB11 / CYCLINC


Mass: 33479.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24863
#3: Chemical ChemComp-C1I / CORTISTATIN A / Cortistatins


Mass: 472.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H36N2O3 / Comment: inhibitor, alkaloid*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.04 Å3/Da / Density % sol: 59.61 % / Description: NONE
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: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.4→85.62 Å / Num. obs: 34548 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.4→2.65 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.45 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RGF

3rgf


Resolution: 2.4→85.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.294 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25633 1115 3.4 %RANDOM
Rwork0.19908 ---
obs0.20095 31676 94.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---0.1 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→85.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 50 103 5170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195062
X-RAY DIFFRACTIONr_bond_other_d0.0020.024795
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9686869
X-RAY DIFFRACTIONr_angle_other_deg1.14310989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01623.478230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46415848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0951529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021191
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2273.5472415
X-RAY DIFFRACTIONr_mcbond_other4.2273.5492416
X-RAY DIFFRACTIONr_mcangle_it5.8835.9673010
X-RAY DIFFRACTIONr_mcangle_other5.8835.973011
X-RAY DIFFRACTIONr_scbond_it5.464.1012647
X-RAY DIFFRACTIONr_scbond_other5.4544.0962644
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8776.6643860
X-RAY DIFFRACTIONr_long_range_B_refined9.11616.2655696
X-RAY DIFFRACTIONr_long_range_B_other9.11616.2675695
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 78 -
Rwork0.301 2392 -
obs--98.25 %
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)
14.8374-3.21771.732.3048-1.1371.7436-0.2387-0.43750.02780.25750.28660.1422-0.2661-0.1366-0.0480.1528-0.02370.07560.1998-0.03230.1819-16.69216.574-16.291
24.41481.0574-0.66881.9779-0.2450.95420.1291-0.36270.13910.2014-0.03-0.0551-0.13560.0812-0.09910.0992-0.02620.00260.1211-0.03630.021712.4747.13-15.375
31.6052-0.5875-0.5972.14530.08663.30770.0782-0.01560.0055-0.07630.03630.08860.0518-0.0985-0.11450.0382-0.0296-0.01510.02730.02720.092-16.31121.615-45.215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 99
2X-RAY DIFFRACTION2A100 - 365
3X-RAY DIFFRACTION3B-3 - 266

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