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- EMDB-22991: Structure of the yeast CKM -

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Basic information

Entry
Database: EMDB / ID: EMD-22991
TitleStructure of the yeast CKM
Map dataStructure of the yeast CKM
Sample
  • Complex: yeast CDK8 complexCyclin-dependent kinase 8
    • Protein or peptide: Meiotic mRNA stability protein kinase SSN3
    • Protein or peptide: RNA polymerase II holoenzyme cyclin-like subunit
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 12
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 13
KeywordsMediator / Transcription / 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 / positive regulation of transcription from RNA polymerase II promoter by galactose / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RNA polymerase II core promoter sequence-specific DNA binding / cyclin-dependent kinase ...negative regulation of filamentous growth / positive regulation of transcription by galactose / CKM complex / nuclear-transcribed mRNA catabolic process, non-stop decay / mediator complex / positive regulation of transcription from RNA polymerase II promoter by galactose / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RNA polymerase II core promoter sequence-specific DNA binding / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / meiotic cell cycle / protein destabilization / transcription coactivator activity / protein kinase activity / phosphorylation / 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, C-terminal / Mediator complex, subunit Med13, N-terminal / Mediator complex subunit 13 C-terminal domain / Mediator complex subunit 13 N-terminal / Mediator complex, subunit Med12 / Transcription mediator complex subunit Med12 / Transcription mediator complex subunit Med12 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, N-terminal / Cyclin, N-terminal domain ...Mediator complex subunit Med13, C-terminal / Mediator complex, subunit Med13, N-terminal / Mediator complex subunit 13 C-terminal domain / Mediator complex subunit 13 N-terminal / Mediator complex, subunit Med12 / Transcription mediator complex subunit Med12 / Transcription mediator complex subunit Med12 / 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 S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLi YC / Chao TC
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kpx
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22991.png

Downloads & links

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Map

FileDownload / File: emd_22991.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the yeast CKM
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.026627915 - 0.054808397
Average (Standard dev.)0.000089291534 (±0.001531911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z410.880410.880410.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0270.0550.000

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Supplemental data

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Half map: half-volume 1

Fileemd_22991_half_map_1.map
Annotationhalf-volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 2

Fileemd_22991_half_map_2.map
Annotationhalf-volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast CDK8 complex

EntireName: yeast CDK8 complexCyclin-dependent kinase 8
Components
  • Complex: yeast CDK8 complexCyclin-dependent kinase 8
    • Protein or peptide: Meiotic mRNA stability protein kinase SSN3
    • Protein or peptide: RNA polymerase II holoenzyme cyclin-like subunit
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 12
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 13

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Supramolecule #1: yeast CDK8 complex

SupramoleculeName: yeast CDK8 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 430 KDa

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Macromolecule #1: Meiotic mRNA stability protein kinase SSN3

MacromoleculeName: Meiotic mRNA stability protein kinase SSN3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 62.940906 KDa
SequenceString: MYNGKDRAQN SYQPMYQRPM QVQGQQQAQS FVGKKNTIGS VHGKAPMLMA NNDVFTIGPY RARKDRMRVS VLEKYEVIGY IAAGTYGKV YKAKRQINSG TNSANGSSLN GTNAKIPQFD STQPKSSSSM DMQANTNALR RNLLKDEGVT PGRIRTTRED V SPHYNSQK ...String:
MYNGKDRAQN SYQPMYQRPM QVQGQQQAQS FVGKKNTIGS VHGKAPMLMA NNDVFTIGPY RARKDRMRVS VLEKYEVIGY IAAGTYGKV YKAKRQINSG TNSANGSSLN GTNAKIPQFD STQPKSSSSM DMQANTNALR RNLLKDEGVT PGRIRTTRED V SPHYNSQK QTLIKKPLTV FYAIKKFKTE KDGVEQLHYT GISQSACREM ALCRELHNKH LTTLVEIFLE RKCVHMVYEY AE HDLLQII HFHSHPEKRM IPPRMVRSIM WQLLDGVSYL HQNWVLHRDL KPANIMVTID GCVKIGDLGL ARKFHNMLQT LYT GDKVVV TIWYRAPELL LGARHYTPAV DLWSVGCIFA ELIGLQPIFK GEEAKLDSKK TVPFQVNQLQ RILEVLGTPD QKIW PYLEK YPEYDQITKF PKYRDNLATW YHSAGGRDKH ALSLLYHLLN YDPIKRIDAF NALEHKYFTE SDIPVSENVF EGLTY KYPA RRIHTNDNDI MNLGSRTKNN TQASGITAGA AANALGGLGV NRRILAAAAA AAAAVSGNNA SDEPSRKKNR R

UniProtKB: Meiotic mRNA stability protein kinase SSN3

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Macromolecule #2: RNA polymerase II holoenzyme cyclin-like subunit

MacromoleculeName: RNA polymerase II holoenzyme cyclin-like subunit / type: protein_or_peptide / ID: 2
Details: Authors introduced a tag to the C-terminus of the chain B protein in the yeast genome. So the promoter of the chain B is still its endogenous promoter. They did not use a plasmid for protein expression
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 41.136512 KDa
SequenceString: MSGSFWTSTQ RHHWQYTKAS LAKERQKLWL LECQLFPQGL NIVMDSKQNG IEQSITKNIP ITHRDLHYDK DYNLRIYCYF LIMKLGRRL NIRQYALATA HIYLSRFLIK ASVREINLYM LVTTCVYLAC KVEECPQYIR TLVSEARTLW PEFIPPDPTK V TEFEFYLL ...String:
MSGSFWTSTQ RHHWQYTKAS LAKERQKLWL LECQLFPQGL NIVMDSKQNG IEQSITKNIP ITHRDLHYDK DYNLRIYCYF LIMKLGRRL NIRQYALATA HIYLSRFLIK ASVREINLYM LVTTCVYLAC KVEECPQYIR TLVSEARTLW PEFIPPDPTK V TEFEFYLL EELESYLIVH HPYQSLKQIV QVLKQPPFQI TLSSDDLQNC WSLINDSYIN DVHLLYPPHI IAVACLFITI SI HGKPTKG SSLASAASEA IRDPKNSSSP VQIAFNRFMA ESLVDLEEVM DTIQEQITLY DHWDKYHEQW IKFLLHTLYL RPA SAISME KRRWKKNFIA VSAANRFKKI SSSGAL

UniProtKB: RNA polymerase II holoenzyme cyclin-like subunit

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Macromolecule #3: Mediator of RNA polymerase II transcription subunit 12

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 12
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 167.049812 KDa
SequenceString: MNNGSGRYLL TPPDDLHPYV PSSKPQEQVY PDFKPWEHTA AEDQILANFV AKGFYHTPMV NFESISARSS VHESLVTQSN ILSQQFDKI IKIREDHINK IPSNSTTTLH GPGFQLPNRI TLTDHRKETW LHELSSSHTS LVKIGKFIPH GLKRRQVIEQ C YLKFIPLK ...String:
MNNGSGRYLL TPPDDLHPYV PSSKPQEQVY PDFKPWEHTA AEDQILANFV AKGFYHTPMV NFESISARSS VHESLVTQSN ILSQQFDKI IKIREDHINK IPSNSTTTLH GPGFQLPNRI TLTDHRKETW LHELSSSHTS LVKIGKFIPH GLKRRQVIEQ C YLKFIPLK RAIWLIKCCY FIEWKSNHKK KRSNAAGADD AISMHLLKDW TDTFVYILEK LIFDMTNHYN DSQQLRTWKR QI SYFLKLL GNCYSLRLIN KEIFHHWLVE FINKMENFEF LPLSLHILMI FWNDICQIDT NAPVAATITS SQKEPFFLVT KIT DMLLHK YYIVSSSKSM INDENYIIND IKKNNKIKLN ILKILSSLIL KIFQEQSLEV FIFPTSNWEI YKPLLFEIVS NADT NQNSD MKKKLELISY RNESLKNNSS IRNVIMSASN ANDFQLTIVT CKQFPKLSCI QLNCIDTQFT KLLDDNPTEF DWPTY VDQN PLTMHKIIQL ILWSIHPSRQ FDHYESNQLV AKLLLLRINS TDEDLHEFQI EDAIWSLVFQ LAKNFSAQKR VVSYMM PSL YRLLNILITY GIIKVPTYIR KLISSGLLYL QDSNDKFVHV QLLINLKISP LMKSQYNMVL RNVMEYDVKF YEIFNFD QL VEITEQIKMR ILSNDITNLQ LSKTPLSIKI MVAEWYLSHL CSGILSSVNR TVLLKIFKIF CIDLEVFHHF FKWIEFIV Y HQLLSDIESL EALMDILLCY QKLFSQFIND HILFTKTFIF IYKKVLKEKD VPAYNVTSFM PFWKFFMKNF PFVLKVDND LRIELQSVYN DEKLKTEKLK NDKSEVLKVY SMINNSNQAV GQTWNFPEVF QVNIRFLLHN SEIIDTNTSK QFQKARNNVM LLIATNLKE YNKFMSIFLK RKDFTNKNLI QLISLKLLTF EVTQNVLGLE YIIRLLPINL ENNDGSYGLF LKYHKEQFIK S NFEKILLT CYELEKKYHG NECEINYYEI LLKILITYGS SPKLLATSTK IIMLLLNDSV ENSSNILEDI LYYSTCPSET DL NDIPLGS GQPDNDTVVT NDDKSDDDDH TVDEIDHVEY YVMMDFANLW VFQAFTCFCI KKIMENNEPA MAMEDLKNFI FQI IEITNS NDLCSQIFDQ LKDMQTIEMI TQIVEKDFCT SCLQNNNQKI DDNYIVVVIE IITSLSMRFQ RETSGMIVIS MENY HLLIK IIRQLSELNE GNLSKREIQI DAVLKIFSFH QDSIFQRIIA DLSADKPTSP FIDSICKLFD KISFNLRLKL FLYEI LSSL KSFAIYSSTI DAPAFHTSGK VELPKKLLNL PPFQVSSFVK ETKLHSGDYG EEEDADQEES FSLNLGIGIV EIAHEN EQK WLIYDKKDHK YVCTFSMEPY HFISNYNTKY TDDMATGSND TTAFNDSCVN LSLFDARFER KNPH

UniProtKB: Mediator of RNA polymerase II transcription subunit 12

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Macromolecule #4: Mediator of RNA polymerase II transcription subunit 13

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 13
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 160.175156 KDa
SequenceString: MSSDASTYRL EDVLSSFYRV EKIKKINYHQ YISKAQNDQW SIQMEFMLRK QDPKTLVALL SRDLWCFSIN DDPVPTPPAI EHKPVSPDK IGTFTADYSK PNLPPHYALF LKALRRKIYI NLALGSHNKL IQFGNACISL SGVPNYLVQL EPHLFVNGDL T VSLCAKNM ...String:
MSSDASTYRL EDVLSSFYRV EKIKKINYHQ YISKAQNDQW SIQMEFMLRK QDPKTLVALL SRDLWCFSIN DDPVPTPPAI EHKPVSPDK IGTFTADYSK PNLPPHYALF LKALRRKIYI NLALGSHNKL IQFGNACISL SGVPNYLVQL EPHLFVNGDL T VSLCAKNM GLVPMKEENL EESFLSKHAL YLAPSGIRMH LAPASKQGYL ITPPKHTELL LTTLSVSHGI NLQNKKNLKW VA VVPDLGH LNGHTPTIAS YLTPLLEAKK LVWPLHLIFA QPVADIENST SGDPSEFHCL QDALDAIDDF IQLKQTAAYR TPG SSGVLS SNIAGTNPLS SDGAYTEQFQ HYKNNSISSQ PASYHSVQET NKISPKDFSP NFTGIDKLML SPSDQFAPAF LNTP NNNIN ENELFNDRKQ TTVSNDLENS PLKTELEANG RSLEKVNNSV SKTGSVDTLH NKEGTLEQRE QNENLPSDKS DSMVD KELF GEDEDEDLFG DSNKSNSTNE SNKSISDEIT EDMFEMSDEE ENNNNKSINK NNKEMHTDLG KDIPFFPSSE KPNIRT MSG TTKRLNGKRK YLDIPIDEMT LPTSPLYMDP GAPLPVETPR DRRKSVFAPL NFNPIIENNV DNKYKSGGKF SFSPLQK EE ALNFDISMAD LSSSEEEEDE EENGSSDEDL KSLNVRDDMK PSDNISTNTN IHEPQYINYS SIPSLQDSII KQENFNSV N DANITSNKEG FNSIWKIPQN DIPQTESPLK TVDSSIQPIE SNIKMTLEDN NVTSNPSEFT PNMVNSEISN LPKDKSGIP EFTPADPNLS FESSSSLPFL LRHMPLASIP DIFITPTPVV TISEKEQDIL DLIAEQVVTD YNILGNLGIP KIAYRGVKDC QEGLITTTM LQLFSTFDRL NGNDTISKFY NMKQPYVFVK KHHELIKVKH DSQPFIKFLN FRPPNGIKNF KSLLLSSSFK E DCLSFAPT LSQTYINQEL GFCELLKLTN EDPPGLMYLK AFDKNKLLLL AAQIVSYCSN NKNSIKNVPP ILIILPLDNA TL TELVDKA NIFQVIKNEV CAKMPNIELY LKVIPMDFIR NVLVTVDQYV NVAISIYNML PPKSVKFTHI AHTLPEKVNF RTM QQQQMQ QQQQQQQQQQ NNSTGSSSII YYDSYIHLAY SRSVDKEWVF AALSDSYGQG SMTKTWYVGN SRGKFDDACN QIWN IALNL ASKKFGKICL ILTRLNGILP DDELMNWRRL SGRNIHLAVV CVDDNSKISF IDEDKLYPSF KPIYKDTRFG GRMDM TRLY DYEIRDIDQD IHGIVFQHPF PLAHSQHRCA IRSGALIKFK KCDGDTVWDK FAVNLLNCPH SDSTQLLETI LEEFRN LAA LNVWYGLSDG EDGHIPWHIL AVKKMMNTLV HTRVKIANTS AATVHTATSS SIILSDK

UniProtKB: Mediator of RNA polymerase II transcription subunit 13

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: 25 mM Hepes pH 7.4, 200 mM NaCl, and 0.005% NP-40
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 815542
Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138178
FSC plot (resolution estimation)

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