7OHA

nucleosome with TBP and TFIIA bound at SHL +2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures and implications of TBP-nucleosome complexes.

Wang, H.Xiong, L.Cramer, P.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2108859118
  • Primary Citation of Related Structures:  
    7OH9, 7OHA, 7OHB, 7OHC

  • PubMed Abstract: 

    The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at gene promoters. TBP binds and bends DNA, and directs adjacent binding of the transcription factors TFIIA and TFIIB for PIC assembly. Here, we show that yeast TBP can bind to a nucleosome containing the Widom-601 sequence and that TBP-nucleosome binding is stabilized by TFIIA. We determine three cryo-electron microscopy (cryo-EM) structures of TBP-nucleosome complexes, two of them containing also TFIIA. TBP can bind to superhelical location (SHL) -6, which contains a TATA-like sequence, but also to SHL +2, which is GC-rich. Whereas binding to SHL -6 can occur in the absence of TFIIA, binding to SHL +2 is only observed in the presence of TFIIA and goes along with detachment of upstream terminal DNA from the histone octamer. TBP-nucleosome complexes are sterically incompatible with PIC assembly, explaining why a promoter nucleosome generally impairs transcription and must be moved before initiation can occur.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-binding protein240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT15
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunit171Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5691SCNYR20_0002031500SCP684_0003030900
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2122Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3356PACBIOSEQ_LOCUS3547PACBIOSEQ_LOCUS3591PACBIOSEQ_LOCUS3602PACBIOSEQ_LOCUS3607PACBIOSEQ_LOCUS3639PACBIOSEQ_LOCUS3680PACBIOSEQ_LOCUS3892PACBIOSEQ_LOCUS3963
UniProt
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (122-MER)145synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (122-MER)145synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB860, SPP2191, EXC 2067/1-390729940
European Research Council (ERC)European Union882357

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references