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- PDB-8t1l: Atomic model of the mammalian mouse Mediator complex with CKM module -

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Basic information

Entry
Database: PDB / ID: 8t1l
TitleAtomic model of the mammalian mouse Mediator complex with CKM module
Components
  • (Mediator of RNA polymerase II transcription subunit ...) x 25
  • Unknown
KeywordsGENE REGULATION / mouse mediator / CKM module
Function / homology
Function and homology information


positive regulation of T cell extravasation / Nuclear Receptor transcription pathway / CKM complex / negative regulation of smooth muscle cell differentiation / 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 ...positive regulation of T cell extravasation / Nuclear Receptor transcription pathway / CKM complex / negative regulation of smooth muscle cell differentiation / 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 / Regulation of lipid metabolism by PPARalpha / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / Cytoprotection by HMOX1 / core mediator complex / Estrogen-dependent gene expression / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / positive regulation of hepatocyte proliferation / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / camera-type eye development / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / nuclear thyroid hormone receptor binding / lens development in camera-type eye / limb development / embryonic hemopoiesis / triglyceride homeostasis / mammary gland epithelial cell proliferation / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cortical actin cytoskeleton / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of neuron differentiation / LBD domain binding / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / erythrocyte development / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / skeletal muscle cell differentiation / general transcription initiation factor binding / blastocyst development / somatic stem cell population maintenance / animal organ regeneration / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / ubiquitin ligase complex / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / negative regulation of fibroblast proliferation / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / lactation / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / positive regulation of erythrocyte differentiation / cholesterol homeostasis / animal organ morphogenesis / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator activity / mRNA transcription by RNA polymerase II / promoter-specific chromatin binding / chromatin DNA binding / positive regulation of transcription elongation by RNA polymerase II / liver development / protein-DNA complex / brain development / transcription coactivator binding / cell morphogenesis / protein import into nucleus / ubiquitin protein ligase activity / transcription corepressor activity / actin binding / heart development / angiogenesis / transcription regulator complex / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cytoskeleton / transcription coactivator activity / protein ubiquitination / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
Similarity search - Function
MID domain of medPIWI / MID domain of medPIWI / Mediator complex subunit Med13, C-terminal / : / Mediator complex subunit 13 C-terminal domain / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 ...MID domain of medPIWI / MID domain of medPIWI / Mediator complex subunit Med13, C-terminal / : / Mediator complex subunit 13 C-terminal domain / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25 von Willebrand factor type A / 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 / Med14 RM domain / Med14 RM domain / Med14 C-terminal domain / 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 / Coactivator CBP, KIX domain superfamily / von Willebrand factor A-like domain superfamily / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 13 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 23 / Mediator of RNA polymerase II transcription subunit 25 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 6 ...Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 13 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 23 / Mediator of RNA polymerase II transcription subunit 25 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 30 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 29 / Mediator of RNA polymerase II transcription subunit 20
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.83 Å
AuthorsZhao, H. / Asturias, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-67167 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: Mol Cell / Year: 2024
Title: An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II.
Authors: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / ...Authors: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / Srinivas Ramachandran / Robert G Roeder / Yi Shi / Rafael Casellas / Francisco J Asturias /
Abstract: The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent ...The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
History
DepositionJun 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jan 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Mediator of RNA polymerase II transcription subunit 8
A: Mediator of RNA polymerase II transcription subunit 1
B: Mediator of RNA polymerase II transcription subunit 4
C: Mediator of RNA polymerase II transcription subunit 6
D: Mediator of RNA polymerase II transcription subunit 7
F: Mediator of RNA polymerase II transcription subunit 9
G: Mediator of RNA polymerase II transcription subunit 10
H: Mediator of RNA polymerase II transcription subunit 11
I: Mediator of RNA polymerase II transcription subunit 14
J: Mediator of RNA polymerase II transcription subunit 15
K: Mediator of RNA polymerase II transcription subunit 16
L: Mediator of RNA polymerase II transcription subunit 17
M: Mediator of RNA polymerase II transcription subunit 18
O: Mediator of RNA polymerase II transcription subunit 20
P: Mediator of RNA polymerase II transcription subunit 21
Q: Mediator of RNA polymerase II transcription subunit 22
R: Mediator of RNA polymerase II transcription subunit 23
S: Mediator of RNA polymerase II transcription subunit 24
T: Mediator of RNA polymerase II transcription subunit 25
V: Mediator of RNA polymerase II transcription subunit 27
W: Mediator of RNA polymerase II transcription subunit 28
X: Mediator of RNA polymerase II transcription subunit 29
Y: Mediator of RNA polymerase II transcription subunit 30
Z: Mediator of RNA polymerase II transcription subunit 31
a: Unknown
9: Mediator of RNA polymerase II transcription subunit 13


Theoretical massNumber of molelcules
Total (without water)1,520,95326
Polymers1,520,95326
Non-polymers00
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 ... , 25 types, 25 molecules EABCDFGHIJKLMOPQRSTVWXYZ9

#1: Protein Mediator of RNA polymerase II transcription subunit 8 / Activator-recruited cofactor 32 kDa component / ARC32 / Mediator complex subunit 8


Mass: 29232.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D7W5
#2: Protein Mediator of RNA polymerase II transcription subunit 1 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PBP / ...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


Mass: 167354.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q925J9
#3: Protein Mediator of RNA polymerase II transcription subunit 4 / Mediator complex subunit 4


Mass: 29817.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQA5
#4: Protein Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6


Mass: 28473.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q921D4
#5: Protein Mediator of RNA polymerase II transcription subunit 7 / Cofactor required for Sp1 transcriptional activation subunit 9 / CRSP complex subunit 9 / Mediator ...Cofactor required for Sp1 transcriptional activation subunit 9 / CRSP complex subunit 9 / Mediator complex subunit 7


Mass: 27244.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZB6
#6: Protein Mediator of RNA polymerase II transcription subunit 9 / Mediator complex subunit 9


Mass: 15729.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VCS6
#7: Protein Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10


Mass: 15683.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXU0
#8: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 13147.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8C6
#9: Protein Mediator of RNA polymerase II transcription subunit 14 / Cofactor required for Sp1 transcriptional activation subunit 2 / CRSP complex subunit 2 / Mediator ...Cofactor required for Sp1 transcriptional activation subunit 2 / CRSP complex subunit 2 / Mediator complex subunit 14 / Thyroid hormone receptor-associated protein complex 170 kDa component / Trap170


Mass: 161144.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2ABV5
#10: Protein Mediator of RNA polymerase II transcription subunit 15 / Mediator complex subunit 15 / Positive cofactor 2 glutamine/Q-rich-associated protein / PC2 ...Mediator complex subunit 15 / Positive cofactor 2 glutamine/Q-rich-associated protein / PC2 glutamine/Q-rich-associated protein / mPcqap


Mass: 86682.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q924H2
#11: 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: 91890.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6PGF3
#12: Protein Mediator of RNA polymerase II transcription subunit 17 / Cofactor required for Sp1 transcriptional activation subunit 6 / CRSP complex subunit 6 / Mediator ...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


Mass: 72555.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VCD5
#13: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18


Mass: 23675.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZ82
#14: Protein Mediator of RNA polymerase II transcription subunit 20 / Mediator complex subunit 20 / TRF-proximal protein homolog


Mass: 23213.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R0X0
#15: Protein Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex component SRB7


Mass: 15600.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ39
#16: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Surfeit locus protein 5 / Surf-5


Mass: 22304.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q62276
#17: Protein Mediator of RNA polymerase II transcription subunit 23 / Cofactor required for Sp1 transcriptional activation subunit 3 / CRSP complex subunit 3 / Mediator ...Cofactor required for Sp1 transcriptional activation subunit 3 / CRSP complex subunit 3 / Mediator complex subunit 23 / Protein sur-2 homolog / mSur-2


Mass: 156265.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q80YQ2
#18: Protein Mediator of RNA polymerase II transcription subunit 24 / Mediator complex subunit 24 / Thyroid hormone receptor-associated protein 4 / Thyroid hormone ...Mediator complex subunit 24 / Thyroid hormone receptor-associated protein 4 / Thyroid hormone receptor-associated protein complex 100 kDa component / Trap100 / mTRAP100


Mass: 110106.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99K74
#19: Protein Mediator of RNA polymerase II transcription subunit 25 / Mediator complex subunit 25 / mMED25


Mass: 78173.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VCB2
#20: 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


Mass: 35343.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DB40
#21: Protein Mediator of RNA polymerase II transcription subunit 28 / Mediator complex subunit 28


Mass: 19558.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q920D3
#22: Protein Mediator of RNA polymerase II transcription subunit 29 / Intersex-like protein / Mediator complex subunit 29


Mass: 21027.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DB91
#23: Protein Mediator of RNA polymerase II transcription subunit 30 / Mediator complex subunit 30 / Thyroid hormone receptor-associated protein 6 / Thyroid hormone ...Mediator complex subunit 30 / Thyroid hormone receptor-associated protein 6 / Thyroid hormone receptor-associated protein complex 25 kDa component / Trap25


Mass: 20383.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQI9
#24: Protein Mediator of RNA polymerase II transcription subunit 31 / Mediator complex subunit 31 / Mediator complex subunit SOH1


Mass: 15792.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXU1
#26: Protein Mediator of RNA polymerase II transcription subunit 13 / Thyroid hormone receptor-associated protein 1 / Thyroid hormone receptor-associated protein complex ...Thyroid hormone receptor-associated protein 1 / Thyroid hormone receptor-associated protein complex 240 kDa component / Trap240


Mass: 238831.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5SWW4

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Protein/peptide , 1 types, 1 molecules a

#25: Protein/peptide Unknown


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Details

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: Mouse mediator complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.0 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.9
SpecimenConc.: 0.1 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
EM embeddingMaterial: ice
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Calibrated magnification: 36000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingElectron dose: 22.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIXdev_3758:model refinement
3Leginon9.03image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 4.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111331 / Symmetry type: POINT

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