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- EMDB-41497: Structure of the H-lobe of human MED12 -

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Basic information

Entry
Database: EMDB / ID: EMD-41497
TitleStructure of the H-lobe of human MED12
Map data
Sample
  • Cell: H-lobe of human MED12
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 12
KeywordsTranscription / Mediator / CDK8 / MED12 / CKM.
Function / homology
Function and homology information


axis elongation involved in somitogenesis / embryonic neurocranium morphogenesis / CKM complex / endoderm development / post-anal tail morphogenesis / mediator complex / Generic Transcription Pathway / embryonic brain development / oligodendrocyte development / nuclear vitamin D receptor binding ...axis elongation involved in somitogenesis / embryonic neurocranium morphogenesis / CKM complex / endoderm development / post-anal tail morphogenesis / mediator complex / Generic Transcription Pathway / embryonic brain development / oligodendrocyte development / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / Wnt signaling pathway, planar cell polarity pathway / RSV-host interactions / spinal cord development / somatic stem cell population maintenance / positive regulation of transcription initiation by RNA polymerase II / Schwann cell development / ubiquitin ligase complex / transcription coregulator activity / neural tube closure / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / beta-catenin binding / ubiquitin protein ligase activity / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein ubiquitination / chromatin binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus
Similarity search - Function
Mediator complex, subunit Med12, catenin-binding / Mediator complex, subunit Med12, LCEWAV-domain / : / Eukaryotic Mediator 12 catenin-binding domain / Eukaryotic Mediator 12 subunit domain / Mediator complex, subunit Med12 / Transcription mediator complex subunit Med12 / Transcription mediator complex subunit Med12
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsChen SF / Chao TC / Kim HJ / Tang HC / Khadka S / Li T / Murakami K / Boyer TG / Tsai KL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol Cell / Year: 2024
Title: Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module.
Authors: Ti-Chun Chao / Shin-Fu Chen / Hee Jong Kim / Hui-Chi Tang / Hsiang-Ching Tseng / An Xu / Leon Palao / Subash Khadka / Tao Li / Mo-Fan Huang / Dung-Fang Lee / Kenji Murakami / Thomas G Boyer / Kuang-Lei Tsai /
Abstract: The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex ...The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex formation in a manner repressed by the CKM through mechanisms presently unknown. Herein, we report cryoelectron microscopy structures of the complete human Mediator and its CKM. The CKM binds to multiple regions on cMED through both MED12 and MED13, including a large intrinsically disordered region (IDR) in the latter. MED12 and MED13 together anchor the CKM to the cMED hook, positioning CDK8 downstream and proximal to the transcription start site. Notably, the MED13 IDR obstructs the recruitment of RNA Pol II/MED26 onto cMED by direct occlusion of their respective binding sites, leading to functional repression of cMED-dependent transcription. Combined with biochemical and functional analyses, these structures provide a conserved mechanistic framework to explain the basis for CKM-mediated repression of cMED function.
History
DepositionAug 6, 2023-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41497.png

Downloads & links

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Map

FileDownload / File: emd_41497.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 224 pix.
= 239.68 Å		1.07 Å/pix.
x 224 pix.
= 239.68 Å		1.07 Å/pix.
x 224 pix.
= 239.68 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.023465088 - 0.044056635
Average (Standard dev.)0.0004053331 (±0.0019494307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 239.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41497_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41497_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : H-lobe of human MED12

EntireName: H-lobe of human MED12
Components
  • Cell: H-lobe of human MED12
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 12

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Supramolecule #1: H-lobe of human MED12

SupramoleculeName: H-lobe of human MED12 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mediator of RNA polymerase II transcription subunit 12

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 12
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 243.354891 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MAAFGILSYE HRPLKRPRLG PPDVYPQDPK QKEDELTALN VKQGFNNQPA VSGDEHGSAK NVSFNPAKIS SNFSSIIAEK LRCNTLPDT GRRKPQVNQK DNFWLVTARS QSAINTWFTD LAGTKPLTQL AKKVPIFSKK EEVFGYLAKY TVPVMRAAWL I KMTCAYYA ...String:
MAAFGILSYE HRPLKRPRLG PPDVYPQDPK QKEDELTALN VKQGFNNQPA VSGDEHGSAK NVSFNPAKIS SNFSSIIAEK LRCNTLPDT GRRKPQVNQK DNFWLVTARS QSAINTWFTD LAGTKPLTQL AKKVPIFSKK EEVFGYLAKY TVPVMRAAWL I KMTCAYYA AISETKVKKR HVDPFMEWTQ IITKYLWEQL QKMAEYYRPG PAGSGGCGST IGPLPHDVEV AIRQWDYTEK LA MFMFQDG MLDRHEFLTW VLECFEKIRP GEDELLKLLL PLLLRYSGEF VQSAYLSRRL AYFCTRRLAL QLDGVSSHSS HVI SAQSTS TLPTTPAPQP PTSSTPSTPF SDLLMCPQHR PLVFGLSCIL QTILLCCPSA LVWHYSLTDS RIKTGSPLDH LPIA PSNLP MPEGNSAFTQ QVRAKLREIE QQIKERGQAV EVRWSFDKCQ EATAGFTIGR VLHTLEVLDS HSFERSDFSN SLDSL CNRI FGLGPSKDGH EISSDDDAVV SLLCEWAVSC KRSGRHRAMV VAKLLEKRQA EIEAERCGES EAADEKGSIA SGSLSA PSA PIFQDVLLQF LDTQAPMLTD PRSESERVEF FNLVLLFCEL IRHDVFSHNM YTCTLISRGD LAFGAPGPRP PSPFDDP AD DPEHKEAEGS SSSKLEDPGL SESMDIDPSS SVLFEDMEKP DFSLFSPTMP CEGKGSPSPE KPDVEKEVKP PPKEKIEG T LGVLYDQPRH VQYATHFPIP QEESCSHECN QRLVVLFGVG KQRDDARHAI KKITKDILKV LNRKGTAETD QLAPIVPLN PGDLTFLGGE DGQKRRRNRP EAFPTAEDIF AKFQHLSHYD QHQVTAQVSR NVLEQITSFA LGMSYHLPLV QHVQFIFDLM EYSLSISGL IDFAIQLLNE LSVVEAELLL KSSDLVGSYT TSLCLCIVAV LRHYHACLIL NQDQMAQVFE GLCGVVKHGM N RSDGSSAE RCILAYLYDL YTSCSHLKNK FGELFSDFCS KVKNTIYCNV EPSESNMRWA PEFMIDTLEN PAAHTFTYTG LG KSLSENP ANRYSFVCNA LMHVCVGHHD PDRVNDIAIL CAELTGYCKS LSAEWLGVLK ALCCSSNNGT CGFNDLLCNV DVS DLSFHD SLATFVAILI ARQCLLLEDL IRCAAIPSLL NAACSEQDSE PGARLTCRIL LHLFKTPQLN PCQSDGNKPT VGIR SSCDR HLLAASQNRI VDGAVFAVLK AVFVLGDAEL KGSGFTVTGG TEELPEEEGG GGSGGRRQGG RNISVETASL DVYAK YVLR SICQQEWVGE RCLKSLCEDS NDLQDPVLSS AQAQRLMQLI CYPHRLLDNE DGENPQRQRI KRILQNLDQW TMRQSS LEL QLMIKQTPNN EMNSLLENIA KATIEVFQQS AETGSSSGST ASNMPSSSKT KPVLSSLERS GVWLVAPLIA KLPTSVQ GH VLKAAGEELE KGQHLGSSSR KERDRQKQKS MSLLSQQPFL SLVLTCLKGQ DEQREGLLTS LYSQVHQIVN NWRDDQYL D DCKPKQLMHE ALKLRLNLVG GMFDTVQRST QQTTEWAMLL LEIIISGTVD MQSNNELFTT VLDMLSVLIN GTLAADMSS ISQGSMEENK RAYMNLAKKL QKELGERQSD SLEKVRQLLP LPKQTRDVIT CEPQGSLIDT KGNKIAGFDS IFKKEGLQVS TKQKISPWD LFEGLKPSAP LSWGWFGTVR VDRRVARGEE QQRLLLYHTH LRPRPRAYYL EPLPLPPEDE EPPAPTLLEP E KKAPEPPK TDKPGAAPPS TEERKKKSTK GKKRSQPATK TEDYGMGPGR SGPYGVTVPP DLLHHPNPGS ITHLNYRQGS IG LYTQNQP LPAGGPRVDP YRPVRLPMQK LPTRPTYPGV LPTTMTGVMG LEPSSYKTSV YRQQQPAVPQ GQRLRQQLQQ SQG MLGQSS VHQMTPSSSY GLQTSQGYTP YVSHVGLQQH TGPAGTMVPP SYSSQPYQST HPSTNPTLVD PTRHLQQRPS GYVH QQAPT YGHGLTSTQR FSHQTLQQTP MISTMTPMSA QGVQAGVRST AILPEQQQQQ QQQQQQQQQQ QQQQQQQQQQ QYHIR QQQQ QQILRQQQQQ QQQQQQQQQQ QQQQQQQQQQ QHQQQQQQQA APPQPQPQSQ PQFQRQGLQQ TQQQQQTAAL VRQLQQ QLS NTQPQPSTNI FGRY

UniProtKB: Mediator of RNA polymerase II transcription subunit 12

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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: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68316
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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