7EGB

TFIID-based holo PIC on SCP promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

    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
General transcription factor IIH subunit 1B [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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GTEx:  ENSG00000110768 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2C [auth 2]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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GTEx:  ENSG00000145736 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3D [auth 3]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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GTEx:  ENSG00000111358 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4E [auth 4]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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GTEx:  ENSG00000213780 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5F [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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GTEx:  ENSG00000272047 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBG [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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDH [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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7I [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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HJ [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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GTEx:  ENSG00000134480 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1K [auth A]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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2L [auth B]1,199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4FA [auth d],
M [auth D]
1,085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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GTEx:  ENSG00000130699 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5GA [auth e],
N [auth E]
800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
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GTEx:  ENSG00000148835 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6HA [auth f],
O [auth F]
677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
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GTEx:  ENSG00000106290 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7P [auth G]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
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GTEx:  ENSG00000178913 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8Q [auth H]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
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GTEx:  ENSG00000137413 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9IA [auth i],
R [auth I]
264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
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GTEx:  ENSG00000273841 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10JA [auth j],
S [auth J]
218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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GTEx:  ENSG00000166337 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12LA [auth l],
T [auth L]
161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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GTEx:  ENSG00000120656 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2U [auth O]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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GTEx:  ENSG00000140307 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinV [auth P]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1W [auth Q]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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GTEx:  ENSG00000165417 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBX [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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1Y [auth S]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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GTEx:  ENSG00000125651 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2Z [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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1AA [auth U]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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GTEx:  ENSG00000153767 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaBA [auth V]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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GTEx:  ENSG00000197265 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3EA [auth c]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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GTEx:  ENSG00000165632 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11KA [auth k]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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GTEx:  ENSG00000064995 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13MA [auth m]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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GTEx:  ENSG00000197780 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1NA [auth o]1,970Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaOA [auth p]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3PA [auth q]275Sus scrofaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4QA [auth r]142Sus scrofaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit ERA [auth s]210Sus scrofaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FSA [auth t]127Sus scrofaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7TA [auth u]172Sus scrofaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3UA [auth v]150Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCB2 (Sus scrofa)
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UniProt GroupI3LCB2
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9VA [auth w]125Sus scrofaMutation(s): 0 
UniProt
Find proteins for P60899 (Sus scrofa)
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UniProt GroupP60899
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
RPB10WA [auth x]67Sus scrofaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinXA [auth y]117Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
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UniProt GroupF1RKE4
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
RPB12YA [auth z]58Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
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Entity ID: 29
MoleculeChains LengthOrganismImage
DNA (69-MER)CA [auth X]94Homo sapiens
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Entity ID: 30
MoleculeChains LengthOrganismImage
DNA (69-MER)DA [auth Y]69Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
GB [auth 7]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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AB [auth 0]
BB [auth 2]
CB [auth 2]
DB [auth 2]
EB [auth 3]
AB [auth 0],
BB [auth 2],
CB [auth 2],
DB [auth 2],
EB [auth 3],
FB [auth 3],
HB [auth R],
IB [auth U],
JB [auth o],
KB [auth o],
MB [auth p],
NB [auth q],
OB [auth w],
PB [auth w],
QB [auth x],
RB [auth z],
ZA [auth 0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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LB [auth o]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

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
  • Version 2.0: 2023-07-26
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary