7EG7

TFIID-based core PIC on SCP promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 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

Structural insights into preinitiation complex assembly on core promoters.

Chen, X.Qi, Y.Wu, Z.Wang, X.Li, J.Zhao, D.Hou, H.Li, Y.Yu, Z.Liu, W.Wang, M.Ren, Y.Li, Z.Yang, H.Xu, Y.

(2021) Science 372

  • DOI: https://doi.org/10.1126/science.aba8490
  • Primary Citation of Related Structures:  
    7EDX, 7EG7, 7EG8, 7EG9, 7EGA, 7EGB, 7EGC, 7EGD, 7EGE, 7EGF, 7EGG, 7EGH, 7EGI, 7EGJ

  • PubMed Abstract: 

    Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering 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
Transcription initiation factor TFIID subunit 11,872Homo 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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PHAROS:  P21675
GTEx:  ENSG00000147133 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 21,199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
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PHAROS:  Q6P1X5
GTEx:  ENSG00000064313 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4C [auth D],
T [auth d]
1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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GTEx:  ENSG00000130699 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5D [auth E],
U [auth e]
800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
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GTEx:  ENSG00000148835 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6E [auth F],
V [auth f]
677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
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GTEx:  ENSG00000106290 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7F [auth G]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
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GTEx:  ENSG00000178913 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8G [auth H]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
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GTEx:  ENSG00000137413 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9H [auth I],
W [auth i]
264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
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GTEx:  ENSG00000273841 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10I [auth J],
X [auth j]
218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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GTEx:  ENSG00000166337 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12J [auth L],
Z [auth l]
161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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GTEx:  ENSG00000120656 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2K [auth O]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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GTEx:  ENSG00000140307 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinL [auth P]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1M [auth Q]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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GTEx:  ENSG00000165417 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBN [auth R]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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GTEx:  ENSG00000137947 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1O [auth S]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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GTEx:  ENSG00000125651 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2P [auth T]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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GTEx:  ENSG00000188342 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3S [auth c]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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GTEx:  ENSG00000165632 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11Y [auth k]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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GTEx:  ENSG00000064995 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13AA [auth m]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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GTEx:  ENSG00000197780 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1BA [auth o]1,970Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCA [auth p]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3DA [auth q]275Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4EA [auth r]142Sus scrofaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EFA [auth s]210Sus scrofaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FGA [auth t]127Sus scrofaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3HA [auth v]150Sus scrofaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9IA [auth w]125Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RPB10JA [auth x]67Sus scrofaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinKA [auth y]117Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RPB12LA [auth z]58Sus scrofaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7MA [auth u]172Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (79-MER)Q [auth X]79Homo sapiens
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Entity ID: 18
MoleculeChains LengthOrganismImage
DNA (79-MER)R [auth Y]79Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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NA [auth R]
OA [auth o]
PA [auth o]
RA [auth p]
SA [auth q]
NA [auth R],
OA [auth o],
PA [auth o],
RA [auth p],
SA [auth q],
TA [auth w],
UA [auth w],
VA [auth x],
WA [auth z]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
QA [auth o]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references