6XJF

X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha (SeMet labeled protein)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase.

Jun, S.H., Hyun, J., Cha, J.S., Kim, H., Bartlett, M.S., Cho, H.S., Murakami, K.S.

(2020) Nat Commun 11: 6123-6123

  • DOI: https://doi.org/10.1038/s41467-020-19998-x
  • Primary Citation of Related Structures:  
    6KF3, 6KF4, 6KF9, 6PLN, 6XJF

  • PubMed Abstract: 

    Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.

    • Organizational Affiliation: 

    Electron Microscopy Research Center, Korea Basic Science Institute, Chungcheongbukdo, 28119, Republic of Korea. jsh100@kbsi.re.kr.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor E
A, B, C, D, E
A, B, C, D, E, F, G, H
110Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: tfe, PF0491
UniProt
Find proteins for Q8U3H5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3H5 
Go to UniProtKB:  Q8U3H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3H5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.199α = 90
b = 115.61β = 90
c = 124.209γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM131860

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references