7ENC

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.13 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

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1A [auth a]1,581Homo sapiensMutation(s): 0 
Gene Names: MED1
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GTEx:  ENSG00000125686 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31B [auth m]131Homo sapiensMutation(s): 0 
Gene Names: MED31
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GTEx:  ENSG00000108590 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4C [auth d]270Homo sapiensMutation(s): 0 
Gene Names: MED4
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GTEx:  ENSG00000136146 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6D [auth f]246Homo sapiensMutation(s): 0 
Gene Names: MED6
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GTEx:  ENSG00000133997 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7E [auth g]233Homo sapiensMutation(s): 0 
Gene Names: MED7
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GTEx:  ENSG00000155868 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 8F [auth h]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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GTEx:  ENSG00000159479 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18G [auth r]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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GTEx:  ENSG00000130772 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20H [auth t]212Homo sapiensMutation(s): 0 
Gene Names: MED20
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GTEx:  ENSG00000124641 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10I [auth j]135Homo sapiensMutation(s): 0 
Gene Names: MED10
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GTEx:  ENSG00000133398 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11J [auth k]117Homo sapiensMutation(s): 0 
Gene Names: MED11
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GTEx:  ENSG00000161920 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14K [auth n]1,454Homo sapiensMutation(s): 0 
Gene Names: MED14
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GTEx:  ENSG00000180182 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17L [auth q]651Homo sapiensMutation(s): 0 
Gene Names: MED17
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GTEx:  ENSG00000042429 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19M [auth s]244Homo sapiensMutation(s): 0 
Gene Names: MED19
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GTEx:  ENSG00000156603 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21N [auth u]144Homo sapiensMutation(s): 0 
Gene Names: MED21
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GTEx:  ENSG00000152944 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22O [auth v]200Homo sapiensMutation(s): 0 
Gene Names: MED22
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GTEx:  ENSG00000148297 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 26P [auth z]600Homo sapiensMutation(s): 0 
Gene Names: MED26
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GTEx:  ENSG00000105085 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27Q [auth c]311Homo sapiensMutation(s): 0 
Gene Names: MED27
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GTEx:  ENSG00000160563 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28R [auth e]178Homo sapiensMutation(s): 0 
Gene Names: MED28
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GTEx:  ENSG00000118579 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29S [auth b]200Homo sapiensMutation(s): 0 
Gene Names: MED29
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GTEx:  ENSG00000063322 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30T [auth l]178Homo sapiensMutation(s): 0 
Gene Names: MED30
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GTEx:  ENSG00000164758 
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UniProt GroupQ96HR3
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15U [auth o]788Homo sapiensMutation(s): 0 
Gene Names: MED15
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GTEx:  ENSG00000099917 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9V [auth i]146Homo sapiensMutation(s): 0 
Gene Names: MED9
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GTEx:  ENSG00000141026 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1W [auth 0]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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GTEx:  ENSG00000020426 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7X [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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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HY [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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GTEx:  ENSG00000134480 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1Z [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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GTEx:  ENSG00000110768 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2AA [auth 2]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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GTEx:  ENSG00000145736 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3BA [auth 3]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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GTEx:  ENSG00000111358 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4CA [auth 4]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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GTEx:  ENSG00000213780 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5DA [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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GTEx:  ENSG00000272047 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBEA [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: 32
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDFA [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: 33
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1GA [auth EA]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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GTEx:  ENSG00000153767 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaHA [auth EB]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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GTEx:  ENSG00000197265 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1IA [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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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2JA [auth DB]1,199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
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GTEx:  ENSG00000064313 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4KA [auth DD],
TA [auth Dd]
1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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PHAROS:  O00268
GTEx:  ENSG00000130699 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5LA [auth DE],
UA [auth De]
800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
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Find proteins for Q15542 (Homo sapiens)
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GTEx:  ENSG00000148835 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6MA [auth DF],
VA [auth Df]
677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
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Find proteins for P49848 (Homo sapiens)
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GTEx:  ENSG00000106290 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7NA [auth DG]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
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Find proteins for Q15545 (Homo sapiens)
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GTEx:  ENSG00000178913 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8OA [auth DH]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
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Find proteins for Q7Z7C8 (Homo sapiens)
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GTEx:  ENSG00000137413 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9PA [auth DI],
WA [auth Di]
264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
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Find proteins for Q16594 (Homo sapiens)
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GTEx:  ENSG00000273841 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10QA [auth DJ],
XA [auth Dj]
218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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Find proteins for Q12962 (Homo sapiens)
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GTEx:  ENSG00000166337 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12RA [auth DL],
ZA [auth Dl]
161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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Find proteins for Q16514 (Homo sapiens)
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GTEx:  ENSG00000120656 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3SA [auth Dc]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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Find proteins for Q5VWG9 (Homo sapiens)
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GTEx:  ENSG00000165632 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11YA [auth Dk]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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Find proteins for Q15544 (Homo sapiens)
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GTEx:  ENSG00000064995 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13AB [auth Dm]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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GTEx:  ENSG00000197780 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2BB [auth DO]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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Find proteins for P52657 (Homo sapiens)
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GTEx:  ENSG00000140307 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinCB [auth DP]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Find proteins for P20226 (Homo sapiens)
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GTEx:  ENSG00000112592 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIA-aDB [auth DQ]307Homo sapiensMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBEB [auth BA]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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Find proteins for Q00403 (Homo sapiens)
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GTEx:  ENSG00000137947 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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Find proteins for P13984 (Homo sapiens)
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GTEx:  ENSG00000188342 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1IB [auth PA]1,970Sus scrofaMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaJB [auth PB]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A4X1TVZ5 (Sus scrofa)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3KB [auth PC]275Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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UniProt GroupI3LCH3
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4LB [auth PD]142Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A481BYI6 (Sus scrofa)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EMB [auth PE]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VTX4 (Sus scrofa)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FNB [auth PF]127Sus scrofaMutation(s): 0 
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