9BCT

Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis of archaeal FttA-dependent transcription termination.

You, L.Wang, C.Molodtsov, V.Kuznedelov, K.Miao, X.Wenck, B.R.Ulisse, P.Sanders, T.J.Marshall, C.J.Firlar, E.Kaelber, J.T.Santangelo, T.J.Ebright, R.H.

(2024) Nature 635: 229-236

  • DOI: https://doi.org/10.1038/s41586-024-07979-9
  • Primary Citation of Related Structures:  
    9BCT, 9BCU

  • PubMed Abstract: 

    The ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea 1-3 . Here we report the structure of a Thermococcus kodakarensis transcription pre-termination complex comprising FttA, Spt4, Spt5 and a transcription elongation complex (TEC). The structure shows that FttA interacts with the TEC in a manner that enables RNA to proceed directly from the TEC RNA-exit channel to the FttA catalytic centre and that enables endonucleolytic cleavage of RNA by FttA, followed by 5'→3' exonucleolytic cleavage of RNA by FttA and concomitant 5'→3' translocation of FttA on RNA, to apply mechanical force to the TEC and trigger termination. The structure further reveals that Spt5 bridges FttA and the TEC, explaining how Spt5 stimulates FttA-dependent termination. The results reveal functional analogy between bacterial and archaeal factor-dependent termination, functional homology between archaeal and eukaryotic factor-dependent termination, and fundamental mechanistic similarities in factor-dependent termination in bacteria, archaea, and eukaryotes.


  • Organizational Affiliation

    Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit A'906Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE33 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit B1,123Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit A"391Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE34 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit D261Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JJF4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit E190Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit F122Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JI52 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit HG [auth H]82Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE31 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit KH [auth K]60Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JJD0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit LI [auth L]94Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JE88 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit NJ [auth N]65Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JJC9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit PK [auth P]49Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5JDM8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor Spt5L [auth G]152Thermococcus kodakarensisMutation(s): 0 
Gene Names: spt5
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor Spt4M [auth I]73Thermococcus kodakarensisMutation(s): 0 
Gene Names: spt4TK1698
UniProt
Find proteins for Q5JIY5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor FttAN [auth J],
O [auth M]
648Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK1428
EC: 3.1
UniProt
Find proteins for Q5JH24 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 15
MoleculeChains LengthOrganismImage
non-template strand DNAP [auth 5]36synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
template strand DNAQ [auth 6]36synthetic construct
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Entity ID: 17
MoleculeChains LengthOrganismImage
RNAR [auth 7]44synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth M]
T [auth A]
U [auth A]
V [auth B]
W [auth N]
AA [auth M],
T [auth A],
U [auth A],
V [auth B],
W [auth N],
X [auth P],
Y [auth I],
Z [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
S [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references