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- PDB-7kpv: Structure of kinase and Central lobes of yeast CKM -

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Basic information

Entry
Database: PDB / ID: 7kpv
TitleStructure of kinase and Central lobes of yeast CKM
Components
  • Mediator of RNA polymerase II transcription subunit 12
  • Mediator of RNA polymerase II transcription subunit 13
  • Meiotic mRNA stability protein kinase SSN3
  • RNA polymerase II holoenzyme cyclin-like subunit
KeywordsTRANSCRIPTION / Mediator / Kinase / Cdk8 / Med13 / Med12 / CycC / CDK / Argonaute / RNA Polymerase II / PIWI.
Function / homology
Function and homology information


negative regulation of filamentous growth / positive regulation of transcription by galactose / CKM complex / nuclear-transcribed mRNA catabolic process, non-stop decay / mediator complex / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II core promoter sequence-specific DNA binding ...negative regulation of filamentous growth / positive regulation of transcription by galactose / CKM complex / nuclear-transcribed mRNA catabolic process, non-stop decay / mediator complex / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / meiotic cell cycle / protein destabilization / cellular response to heat / transcription coactivator activity / protein kinase activity / protein serine kinase activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus
Similarity search - Function
Mediator complex, subunit Med13, N-terminal / Mediator complex subunit 13 N-terminal / Mediator complex, subunit Med12 / Transcription mediator complex subunit Med12 / Transcription mediator complex subunit Med12 / Mediator complex subunit Med13, C-terminal / : / Mediator complex subunit 13 C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, N-terminal ...Mediator complex, subunit Med13, N-terminal / Mediator complex subunit 13 N-terminal / Mediator complex, subunit Med12 / Transcription mediator complex subunit Med12 / Transcription mediator complex subunit Med12 / Mediator complex subunit Med13, C-terminal / : / Mediator complex subunit 13 C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 12 / Mediator of RNA polymerase II transcription subunit 13 / Meiotic mRNA stability protein kinase SSN3 / RNA polymerase II holoenzyme cyclin-like subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi, Y.C. / Chao, T.C. / Kim, H.J. / Cholko, T. / Chen, S.F. / Nakanishi, K. / Chang, C.E. / Murakami, K. / Garcia, B.A. / Boyer, T.G. / Tsai, K.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)13127 United States
CitationJournal: Sci Adv / Year: 2021
Title: Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Authors: Yi-Chuan Li / Ti-Chun Chao / Hee Jong Kim / Timothy Cholko / Shin-Fu Chen / Guojie Li / Laura Snyder / Kotaro Nakanishi / Chia-En Chang / Kenji Murakami / Benjamin A Garcia / Thomas G Boyer / Kuang-Lei Tsai /
Abstract: The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic ...The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.
History
DepositionNov 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 27, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Meiotic mRNA stability protein kinase SSN3
B: RNA polymerase II holoenzyme cyclin-like subunit
C: Mediator of RNA polymerase II transcription subunit 12
D: Mediator of RNA polymerase II transcription subunit 13


Theoretical massNumber of molelcules
Total (without water)428,0004
Polymers428,0004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Meiotic mRNA stability protein kinase SSN3 / Cyclin-dependent kinase 8 / Suppressor of RNA polymerase B SRB10


Mass: 62940.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P39073, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein RNA polymerase II holoenzyme cyclin-like subunit / Suppressor of RNA polymerase B 11


Mass: 37834.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47821
#3: Protein Mediator of RNA polymerase II transcription subunit 12 / Mediator complex subunit 12 / Suppressor of RNA polymerase B 8


Mass: 167049.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25648
#4: Protein Mediator of RNA polymerase II transcription subunit 13 / Mediator complex subunit 13 / Protein SCA1 / Suppressor of RNA polymerase B SSN2


Mass: 160175.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38931
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: yeast CDK8 complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.43 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.4 / Details: 25 mM Hepes pH 7.4, 200 mM NaCl, and 0.005% NP-40
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 65 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
4RELIONCTF correction
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31534 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00516873
ELECTRON MICROSCOPYf_angle_d0.89922877
ELECTRON MICROSCOPYf_dihedral_angle_d22.0036262
ELECTRON MICROSCOPYf_chiral_restr0.0552548
ELECTRON MICROSCOPYf_plane_restr0.0072871

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