7ENA

TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of the human Mediator and Mediator-bound preinitiation complex.

Chen, X.Yin, X.Li, J.Wu, Z.Qi, Y.Wang, X.Liu, W.Xu, Y.

(2021) Science 372

  • DOI: https://doi.org/10.1126/science.abg0635
  • Primary Citation of Related Structures:  
    7EMF, 7ENA, 7ENC, 7ENJ

  • PubMed Abstract: 

    The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.


  • Organizational Affiliation

    Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1A [auth 0]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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GTEx:  ENSG00000020426 
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UniProt GroupP51948
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7B [auth 8]346Homo sapiensMutation(s): 0 
Gene Names: CDK7CAKCAK1CDKN7MO15STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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GTEx:  ENSG00000134058 
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UniProt GroupP50613
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HC [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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GTEx:  ENSG00000134480 
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UniProt GroupP51946
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2D [auth DO]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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PHAROS:  P52657
GTEx:  ENSG00000140307 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinE [auth DP]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIA-aF [auth DQ]307Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBG [auth BA]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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GTEx:  ENSG00000137947 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1H [auth FA]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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GTEx:  ENSG00000125651 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2I [auth FB]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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GTEx:  ENSG00000188342 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1J [auth PA]1,970Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaK [auth PB]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3L [auth PC]275Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4M [auth PD]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EN [auth PE]210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FO [auth PF]127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7P [auth PG]172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3Q [auth PH]150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9R [auth PI]125Sus scrofaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RPB10S [auth PJ]67Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinT [auth PK]117Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RPB12U [auth PL]58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1V [auth DA]1,872Homo sapiensMutation(s): 0 
Gene Names: TAF1BA2RCCG1CCGSTAF2A
EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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GTEx:  ENSG00000147133 
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UniProt GroupP21675
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2W [auth DB]1,199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
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GTEx:  ENSG00000064313 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4GA [auth Dd],
X [auth DD]
1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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GTEx:  ENSG00000130699 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5HA [auth De],
Y [auth DE]
800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
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GTEx:  ENSG00000148835 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6IA [auth Df],
Z [auth DF]
677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
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GTEx:  ENSG00000106290 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7AA [auth DG]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
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GTEx:  ENSG00000178913 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8BA [auth DH]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
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GTEx:  ENSG00000137413 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9CA [auth DI],
JA [auth Di]
264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
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GTEx:  ENSG00000273841 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10DA [auth DJ],
KA [auth Dj]
218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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GTEx:  ENSG00000166337 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12EA [auth DL],
MA [auth Dl]
161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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GTEx:  ENSG00000120656 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3FA [auth Dc]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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GTEx:  ENSG00000165632 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11LA [auth Dk]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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GTEx:  ENSG00000064995 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13NA [auth Dm]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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GTEx:  ENSG00000197780 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1OA [auth EA]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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GTEx:  ENSG00000153767 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaPA [auth EB]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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GTEx:  ENSG00000197265 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1QA [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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GTEx:  ENSG00000110768 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2RA [auth 2]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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GTEx:  ENSG00000145736 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3SA [auth 3]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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GTEx:  ENSG00000111358 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4TA [auth 4]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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GTEx:  ENSG00000213780 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5UA [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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GTEx:  ENSG00000272047 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBVA [auth 6]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
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GTEx:  ENSG00000163161 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDWA [auth 7]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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GTEx:  ENSG00000104884 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27XA [auth c]311Homo sapiensMutation(s): 0 
Gene Names: MED27
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GTEx:  ENSG00000160563 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28YA [auth e]178Homo sapiensMutation(s): 0 
Gene Names: MED28
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GTEx:  ENSG00000118579 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29ZA [auth b]200Homo sapiensMutation(s): 0 
Gene Names: MED29
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GTEx:  ENSG00000063322 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30AB [auth l]178Homo sapiensMutation(s): 0 
Gene Names: MED30
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GTEx:  ENSG00000164758 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31BB [auth m]131Homo sapiensMutation(s): 0 
Gene Names: MED31
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GTEx:  ENSG00000108590 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1CB [auth a]1,581Homo sapiensMutation(s): 0 
Gene Names: MED1
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GTEx:  ENSG00000125686 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4DB [auth d]270Homo sapiensMutation(s): 0 
Gene Names: MED4
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GTEx:  ENSG00000136146 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6EB [auth f]246Homo sapiensMutation(s): 0 
Gene Names: MED6
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GTEx:  ENSG00000133997 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7FB [auth g]233Homo sapiensMutation(s): 0 
Gene Names: MED7
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GTEx:  ENSG00000155868 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 8GB [auth h]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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GTEx:  ENSG00000159479 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9HB [auth i]146Homo sapiensMutation(s): 0 
Gene Names: MED9
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GTEx:  ENSG00000141026 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10IB [auth j]135Homo sapiensMutation(s): 0 
Gene Names: MED10
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GTEx:  ENSG00000133398 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11JB [auth k]117Homo sapiensMutation(s): 0 
Gene Names: MED11
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Find proteins for Q9P086 (Homo sapiens)
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GTEx:  ENSG00000161920 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14KB [auth n]1,454Homo sapiensMutation(s): 0 
Gene Names: MED14
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GTEx:  ENSG00000180182 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15LB [auth o]788Homo sapiensMutation(s): 0 
Gene Names: MED15
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GTEx:  ENSG00000099917 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17MB [auth q]651Homo sapiensMutation(s): 0 
Gene Names: MED17
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GTEx:  ENSG00000042429 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18NB [auth r]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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Find proteins for Q9BUE0 (Homo sapiens)
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GTEx:  ENSG00000130772 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19OB [auth s]244Homo sapiensMutation(s): 0 
Gene Names: MED19
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Find proteins for A0JLT2 (Homo sapiens)
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GTEx:  ENSG00000156603 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20PB [auth t]212Homo sapiensMutation(s): 0 
Gene Names: MED20
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Find proteins for Q9H944 (Homo sapiens)
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GTEx:  ENSG00000124641 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21QB [auth u]144Homo sapiensMutation(s): 0 
Gene Names: MED21
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GTEx:  ENSG00000152944 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22RB [auth v]200Homo sapiensMutation(s): 0 
Gene Names: MED22
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GTEx:  ENSG00000148297 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 26SB [auth z]600Homo sapiensMutation(s): 0 
Gene Names: MED26
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Find proteins for O95402 (Homo sapiens)
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GTEx:  ENSG00000105085 
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