5N9G

TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation.

Gouge, J.Guthertz, N.Kramm, K.Dergai, O.Abascal-Palacios, G.Satia, K.Cousin, P.Hernandez, N.Grohmann, D.Vannini, A.

(2017) Nat Commun 8: 130-130

  • DOI: 10.1038/s41467-017-00126-1
  • Primary Citation of Related Structures:  
    5N9G

  • PubMed Abstract: 
  • Initiation of gene transcription by RNA polymerase (Pol) III requires the activity of TFIIIB, a complex formed by Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment of Pol III and to promote the transition from a ...

    Initiation of gene transcription by RNA polymerase (Pol) III requires the activity of TFIIIB, a complex formed by Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment of Pol III and to promote the transition from a closed to an open Pol III pre-initiation complex, a process dependent on the activity of the Bdp1 subunit. Here, we present a crystal structure of a Brf2-TBP-Bdp1 complex bound to DNA at 2.7 Å resolution, integrated with single-molecule FRET analysis and in vitro biochemical assays. Our study provides a structural insight on how Bdp1 is assembled into TFIIIB complexes, reveals structural and functional similarities between Bdp1 and Pol II factors TFIIA and TFIIF, and unravels essential interactions with DNA and with the upstream factor SNAPc. Furthermore, our data support the idea of a concerted mechanism involving TFIIIB and RNA polymerase III subunits for the closed to open pre-initiation complex transition.Transcription initiation by RNA polymerase III requires TFIIIB, a complex formed by Brf1/Brf2, TBP and Bdp1. Here, the authors describe the crystal structure of a Brf2-TBP-Bdp1 complex bound to a DNA promoter and characterize the role of Bdp1 in TFIIIB assembly and pre-initiation complex formation.


    Organizational Affiliation

    The Institute of Cancer Research, London, SW7 3RP, UK. alessandro.vannini@icr.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor IIIB 50 kDa subunitAF377Homo sapiensMutation(s): 0 
Gene Names: BRF2BRFUPRO1470
Find proteins for Q9HAW0 (Homo sapiens)
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Go to UniProtKB:  Q9HAW0
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinBG200Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
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Go to UniProtKB:  P20226
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PHAROS  P20226
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor TFIIIB component B'' homologCH175Homo sapiensMutation(s): 0 
Gene Names: BDP1KIAA1241KIAA1689TFNR
Find proteins for A6H8Y1 (Homo sapiens)
Explore A6H8Y1 
Go to UniProtKB:  A6H8Y1
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PHAROS  A6H8Y1
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA/RNA (27-MER)D, I27Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA/RNA (25-MER)E, J25Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.19α = 90
b = 124.08β = 99.51
c = 88.61γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K014390/1
Cancer Research UKUnited KingdomC47547/A21536
Wellcome TrustUnited Kingdom200818/Z/16/Z

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-08-09
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence