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- PDB-8tqw: Structure of human transcriptional Mediator complex -

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Basic information

Entry
Database: PDB / ID: 8tqw
TitleStructure of human transcriptional Mediator complex
Components
  • (Mediator of RNA polymerase II transcription subunit ...) x 26
  • Cyclin-C
  • Cyclin-dependent kinase 8
  • Unknown Chain
KeywordsTRANSCRIPTION / Mediator / CDK8 / MED12 / MED13 / CKM.
Function / homology
Function and homology information


axis elongation involved in somitogenesis / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / CKM complex / embryonic neurocranium morphogenesis / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition ...axis elongation involved in somitogenesis / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / CKM complex / embryonic neurocranium morphogenesis / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / oligodendrocyte development / post-anal tail morphogenesis / endoderm development / nuclear retinoic acid receptor binding / embryonic brain development / ventricular trabecula myocardium morphogenesis / mediator complex / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / triglyceride homeostasis / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / [RNA-polymerase]-subunit kinase / nuclear thyroid hormone receptor binding / limb development / lens development in camera-type eye / Wnt signaling pathway, planar cell polarity pathway / embryonic hemopoiesis / cyclin-dependent protein serine/threonine kinase regulator activity / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cortical actin cytoskeleton / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / spinal cord development / LBD domain binding / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / skeletal muscle cell differentiation / monocyte differentiation / somatic stem cell population maintenance / general transcription initiation factor binding / blastocyst development / negative regulation of Notch signaling pathway / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of keratinocyte proliferation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / cyclin-dependent kinase / embryonic placenta development / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / erythrocyte development / Schwann cell development / RNA polymerase II preinitiation complex assembly / negative regulation of fibroblast proliferation / cyclin-dependent protein kinase holoenzyme complex / keratinocyte differentiation / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / DNA-directed RNA polymerase activity / cellular response to epidermal growth factor stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / cholesterol homeostasis / liver development / nuclear receptor binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / neural tube closure / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Heme signaling
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 / MID domain of medPIWI / Transcription mediator complex subunit Med12 / MID domain of medPIWI / Transcription mediator complex subunit Med12 ...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 / MID domain of medPIWI / Transcription mediator complex subunit Med12 / MID domain of medPIWI / Transcription mediator complex subunit Med12 / Mediator complex subunit Med13, C-terminal / : / Mediator complex subunit 13 C-terminal domain / Mediator complex, subunit Med19, metazoa / Mediator of RNA pol II transcription subunit 19 / Mediator complex, subunit Med29, metazoa / Mediator complex, subunit Med24, / : / Mediator complex subunit 24 N-terminal / Mediator complex subunit 29 / Mediator complex subunit 16, central helical bridge / Mediator of RNA polymerase II transcription subunit 15 / : / : / ARC105/Med15 mediator subunit N-terminal KIX domain / ARC105/Med15 mediator subunit central domain / ARC105/Med15 mediator subunit C-terminal domain / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med28 / Mediator of RNA polymerase II transcription subunit 9, metazoan / : / : / : / Mediator complex subunit 30 / Mediator complex subunit 28 / Mediator of RNA polymerase II transcription subunit 14, RM2 / Mediator of RNA polymerase II transcription subunit 14, RM8 / Mediator of RNA polymerase II transcription subunit 14, RM6 / Mediator complex, subunit Med23 / Mediator complex subunit 23 / Mediator complex, subunit Med27 / Mediator complex subunit 27 / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / : / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med7 superfmaily / : / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Soluble quinoprotein glucose/sorbosone dehydrogenase / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / : / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Coactivator CBP, KIX domain superfamily / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 19 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / Cyclin-C / Cyclin-dependent kinase 8 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 1 ...Mediator of RNA polymerase II transcription subunit 19 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / Cyclin-C / Cyclin-dependent kinase 8 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 12 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 30 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 29 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 13 / Mediator of RNA polymerase II transcription subunit 23 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsChen, S.F. / Chao, T.C. / Kim, H.J. / Tang, H.C. / Khadka, S. / Li, T. / Murakami, K. / Boyer, T.G. / Tsai, K.L.
Funding support United States, 1items
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 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Mediator of RNA polymerase II transcription subunit 27
1: Mediator of RNA polymerase II transcription subunit 28
2: Mediator of RNA polymerase II transcription subunit 29
3: Mediator of RNA polymerase II transcription subunit 30
4: Mediator of RNA polymerase II transcription subunit 31
A: Mediator of RNA polymerase II transcription subunit 1
B: Unknown Chain
D: Mediator of RNA polymerase II transcription subunit 4
F: Mediator of RNA polymerase II transcription subunit 6
G: Mediator of RNA polymerase II transcription subunit 7
H: Mediator of RNA polymerase II transcription subunit 8
I: Mediator of RNA polymerase II transcription subunit 9
J: Mediator of RNA polymerase II transcription subunit 10
K: Mediator of RNA polymerase II transcription subunit 11
N: Mediator of RNA polymerase II transcription subunit 14
O: Mediator of RNA polymerase II transcription subunit 15
P: Mediator of RNA polymerase II transcription subunit 16
Q: Mediator of RNA polymerase II transcription subunit 17
R: Mediator of RNA polymerase II transcription subunit 18
S: Mediator of RNA polymerase II transcription subunit 19
T: Mediator of RNA polymerase II transcription subunit 20
U: Mediator of RNA polymerase II transcription subunit 21
V: Mediator of RNA polymerase II transcription subunit 22
W: Mediator of RNA polymerase II transcription subunit 23
X: Mediator of RNA polymerase II transcription subunit 24
a: Cyclin-dependent kinase 8
b: Cyclin-C
c: Mediator of RNA polymerase II transcription subunit 12
d: Mediator of RNA polymerase II transcription subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,808,04833
Polymers1,807,78629
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Mediator of RNA polymerase II transcription subunit ... , 26 types, 26 molecules 01234ADFGHIJKNOPQRSTUVWXcd

#1: Protein Mediator of RNA polymerase II transcription subunit 27 / Cofactor required for Sp1 transcriptional activation subunit 8 / CRSP complex subunit 8 / Mediator ...Cofactor required for Sp1 transcriptional activation subunit 8 / CRSP complex subunit 8 / Mediator complex subunit 27 / P37 TRAP/SMCC/PC2 subunit / Transcriptional coactivator CRSP34


Mass: 35478.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2C8
#2: Protein Mediator of RNA polymerase II transcription subunit 28 / Endothelial-derived protein 1 / Mediator complex subunit 28 / Merlin and Grb2-interacting ...Endothelial-derived protein 1 / Mediator complex subunit 28 / Merlin and Grb2-interacting cytoskeletal protein / Magicin / Tumor angiogenesis marker EG-1


Mass: 19540.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H204
#3: Protein Mediator of RNA polymerase II transcription subunit 29 / Intersex-like protein / Mediator complex subunit 29


Mass: 21089.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX70
#4: Protein Mediator of RNA polymerase II transcription subunit 30 / Mediator complex subunit 30 / TRAP/Mediator complex component TRAP25 / Thyroid hormone receptor- ...Mediator complex subunit 30 / TRAP/Mediator complex component TRAP25 / Thyroid hormone receptor-associated protein 6 / Thyroid hormone receptor-associated protein complex 25 kDa component / Trap25


Mass: 20301.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96HR3
#5: Protein Mediator of RNA polymerase II transcription subunit 31 / Mediator complex subunit 31 / Mediator complex subunit SOH1 / hSOH1


Mass: 15826.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C7
#6: Protein Mediator of RNA polymerase II transcription subunit 1 / Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome ...Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TR-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


Mass: 168697.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15648
#8: Protein Mediator of RNA polymerase II transcription subunit 4 / Activator-recruited cofactor 36 kDa component / ARC36 / Mediator complex subunit 4 / TRAP/SMCC/PC2 ...Activator-recruited cofactor 36 kDa component / ARC36 / Mediator complex subunit 4 / TRAP/SMCC/PC2 subunit p36 subunit / Vitamin D3 receptor-interacting protein complex 36 kDa component / DRIP36


Mass: 29781.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NPJ6
#9: Protein Mediator of RNA polymerase II transcription subunit 6 / Activator-recruited cofactor 33 kDa component / ARC33 / Mediator complex subunit 6 / hMed6 / Renal ...Activator-recruited cofactor 33 kDa component / ARC33 / Mediator complex subunit 6 / hMed6 / Renal carcinoma antigen NY-REN-28


Mass: 28464.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75586
#10: Protein Mediator of RNA polymerase II transcription subunit 7 / hMED7 / Activator-recruited cofactor 34 kDa component / ARC34 / Cofactor required for Sp1 ...hMED7 / Activator-recruited cofactor 34 kDa component / ARC34 / Cofactor required for Sp1 transcriptional activation subunit 9 / CRSP complex subunit 9 / Mediator complex subunit 7 / RNA polymerase transcriptional regulation mediator subunit 7 homolog / Transcriptional coactivator CRSP33


Mass: 27285.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43513
#11: Protein Mediator of RNA polymerase II transcription subunit 8 / Activator-recruited cofactor 32 kDa component / ARC32 / Mediator complex subunit 8


Mass: 29112.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96G25
#12: Protein Mediator of RNA polymerase II transcription subunit 9 / Mediator complex subunit 9


Mass: 16422.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWA0
#13: Protein Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10 / Transformation-related gene 17 protein / TRG-17 / Transformation- ...Mediator complex subunit 10 / Transformation-related gene 17 protein / TRG-17 / Transformation-related gene 20 protein / TRG-20


Mass: 15710.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTT4
#14: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 13145.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P086
#15: Protein Mediator of RNA polymerase II transcription subunit 14 / Activator-recruited cofactor 150 kDa component / ARC150 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 150 kDa component / ARC150 / Cofactor required for Sp1 transcriptional activation subunit 2 / CRSP complex subunit 2 / Mediator complex subunit 14 / RGR1 homolog / hRGR1 / Thyroid hormone receptor-associated protein complex 170 kDa component / Trap170 / Transcriptional coactivator CRSP150 / Vitamin D3 receptor-interacting protein complex 150 kDa component / DRIP150


Mass: 160787.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60244
#16: Protein Mediator of RNA polymerase II transcription subunit 15 / Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex ...Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex subunit 15 / Positive cofactor 2 glutamine/Q-rich-associated protein / PC2 glutamine/Q-rich-associated protein / TPA-inducible gene 1 protein / TIG-1 / Trinucleotide repeat-containing gene 7 protein


Mass: 86830.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96RN5
#17: Protein Mediator of RNA polymerase II transcription subunit 16 / Mediator complex subunit 16 / Thyroid hormone receptor-associated protein 5 / Thyroid hormone ...Mediator complex subunit 16 / Thyroid hormone receptor-associated protein 5 / Thyroid hormone receptor-associated protein complex 95 kDa component / Trap95 / Vitamin D3 receptor-interacting protein complex 92 kDa component / DRIP92


Mass: 96908.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2X0
#18: Protein Mediator of RNA polymerase II transcription subunit 17 / Activator-recruited cofactor 77 kDa component / ARC77 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 77 kDa component / ARC77 / Cofactor required for Sp1 transcriptional activation subunit 6 / CRSP complex subunit 6 / Mediator complex subunit 17 / Thyroid hormone receptor-associated protein complex 80 kDa component / Trap80 / Transcriptional coactivator CRSP77 / Vitamin D3 receptor-interacting protein complex 80 kDa component / DRIP80


Mass: 72984.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVC6
#19: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / p28b


Mass: 23693.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUE0
#20: Protein Mediator of RNA polymerase II transcription subunit 19 / Lung cancer metastasis-related protein 1 / Mediator complex subunit 19


Mass: 26321.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0JLT2
#21: Protein Mediator of RNA polymerase II transcription subunit 20 / Mediator complex subunit 20 / TRF-proximal protein homolog / hTRFP


Mass: 23243.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H944
#22: Protein Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex ...Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex component SRB7 / hSrb7


Mass: 15575.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13503
#23: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Surfeit locus protein 5 / Surf-5


Mass: 22243.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15528
#24: Protein Mediator of RNA polymerase II transcription subunit 23 / Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional activation subunit 3 / CRSP complex subunit 3 / Mediator complex subunit 23 / Protein sur-2 homolog / hSur-2 / Transcriptional coactivator CRSP130 / Vitamin D3 receptor-interacting protein complex 130 kDa component / DRIP130


Mass: 156652.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULK4
#25: Protein Mediator of RNA polymerase II transcription subunit 24 / Activator-recruited cofactor 100 kDa component / ARC100 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 100 kDa component / ARC100 / Cofactor required for Sp1 transcriptional activation subunit 4 / CRSP complex subunit 4 / Mediator complex subunit 24 / Thyroid hormone receptor-associated protein 4 / Thyroid hormone receptor-associated protein complex 100 kDa component / Trap100 / hTRAP100 / Vitamin D3 receptor-interacting protein complex 100 kDa component / DRIP100


Mass: 110430.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75448
#28: Protein Mediator of RNA polymerase II transcription subunit 12


Mass: 243354.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q93074
#29: Protein Mediator of RNA polymerase II transcription subunit 13 / Activator-recruited cofactor 250 kDa component / ARC250 / Mediator complex subunit 13 / Thyroid ...Activator-recruited cofactor 250 kDa component / ARC250 / Mediator complex subunit 13 / Thyroid hormone receptor-associated protein 1 / Thyroid hormone receptor-associated protein complex 240 kDa component / Trap240 / Vitamin D3 receptor-interacting protein complex component DRIP250 / DRIP250


Mass: 239535.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UHV7

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Protein , 2 types, 2 molecules ab

#26: Protein Cyclin-dependent kinase 8


Mass: 53368.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49336
#27: Protein Cyclin-C


Mass: 33279.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24863

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Protein/peptide / Non-polymers , 2 types, 5 molecules B

#30: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Protein/peptide Unknown Chain


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Details

Has ligand of interestY
Has protein modificationY

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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: The human transcriptional Mediator complex / Type: COMPLEX
Entity ID: #9, #11, #18, #28-#29, #6, #26, #5, #7, #27, #17, #8, #1, #10, #12-#16, #19-#25, #2-#4
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6348 / Symmetry type: POINT

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