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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor IIIB 50 kDa subunit
A, F
377Homo sapiensMutation(s): 0 
Gene Names: BRF2BRFUPRO1470
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAW0 (Homo sapiens)
Explore Q9HAW0 
Go to UniProtKB:  Q9HAW0
GTEx:  ENSG00000104221 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HAW0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding protein
B, G
200Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
PHAROS:  P20226
GTEx:  ENSG00000112592 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20226
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor TFIIIB component B'' homolog
C, H
175Homo sapiensMutation(s): 0 
Gene Names: BDP1KIAA1241KIAA1689TFNR
UniProt & NIH Common Fund Data Resources
Find proteins for A6H8Y1 (Homo sapiens)
Explore A6H8Y1 
Go to UniProtKB:  A6H8Y1
PHAROS:  A6H8Y1
GTEx:  ENSG00000145734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6H8Y1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA/RNA (27-MER)
D, I
27Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA/RNA (25-MER)
E, J
25Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth H]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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  (Full details and data files)

  • 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
  • Version 1.4: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description