7EG8

TFIID-based core PIC on PUMA promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.40 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: 10.1126/science.aba8490
  • Primary Citation of Related Structures:  
    7EDX, 7EG7, 7EG8, 7EGI, 7EGJ, 7EGC, 7EGD, 7EGA, 7EGB, 7EGG

  • 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) ...

    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

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1A1872Homo sapiensMutation(s): 0 
Gene Names: TAF1BA2RCCG1CCGSTAF2A
EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P21675 (Homo sapiens)
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PHAROS:  P21675
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2B1199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
Find proteins for Q6P1X5 (Homo sapiens)
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PHAROS:  Q6P1X5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4C [auth D], T [auth d]1085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5D [auth E], U [auth e]800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
Find proteins for Q15542 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6E [auth F], V [auth f]677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
Find proteins for P49848 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7F [auth G]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
Find proteins for Q15545 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8G [auth H]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
Find proteins for Q7Z7C8 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9H [auth I], W [auth i]264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
Find proteins for Q16594 (Homo sapiens)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10I [auth J], X [auth j]218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12J [auth L], Z [auth l]161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2K [auth O]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinL [auth P]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1M [auth Q]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBN [auth R]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1O [auth S]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
Find proteins for P35269 (Homo sapiens)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2P [auth T]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
Find proteins for P13984 (Homo sapiens)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3S [auth c]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
Find proteins for Q5VWG9 (Homo sapiens)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11Y [auth k]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13AA [auth m]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
RPB1BA [auth o]1970Sus scrofaMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCA [auth p]1174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3DA [auth q]275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4EA [auth r]142Sus scrofaMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EFA [auth s]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FGA [auth t]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7HA [auth u]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3IA [auth v]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
Find proteins for A0A4X1ULF2 (Sus scrofa)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9JA [auth w]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
RPB10KA [auth x]67Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinLA [auth y]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
RPB12MA [auth z]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 17
MoleculeChainsLengthOrganismImage
DNA (85-MER)Q [auth X]85Homo sapiens
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Entity ID: 18
MoleculeChainsLengthOrganismImage
DNA (85-MER)R [auth Y]85Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NA [auth R] , OA [auth o] , PA [auth o] , RA [auth p] , SA [auth q] , TA [auth w] , UA [auth w] , VA [auth x] , 
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
 Ligand Interaction
MG
Query on MG

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QA [auth o]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.40 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