7OQ4

Cryo-EM structure of the ATV RNAP Inhibitory Protein (RIP) bound to the DNA-binding channel of the host's RNA polymerase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of RNA polymerase inhibition by viral and host factors.

Pilotto, S.Fouqueau, T.Lukoyanova, N.Sheppard, C.Lucas-Staat, S.Diaz-Santin, L.M.Matelska, D.Prangishvili, D.Cheung, A.C.M.Werner, F.

(2021) Nat Commun 12: 5523-5523

  • DOI: https://doi.org/10.1038/s41467-021-25666-5
  • Primary Citation of Related Structures:  
    7OK0, 7OQ4, 7OQY

  • PubMed Abstract: 

    RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.


  • Organizational Affiliation

    RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit A'880Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P11512 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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UniProt GroupP11512
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit B1,126Sulfolobus acidocaldarius DSM 639Mutation(s): 1 
EC: 2.7.7.6
UniProt
Find proteins for P11513 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit A''393Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P11514 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit D264Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P39471 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit E183Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P39466 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit F114Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q4JB12 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit G130Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
Gene Names: rpoGSaci_0661
EC: 2.7.7.6
UniProt
Find proteins for Q4JAY4 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit H84Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P11521 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit KI [auth K]89Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P39463 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit LJ [auth L]90Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P46217 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit NK [auth N]66Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit PL [auth P]48Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q4JAE8 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved proteinM [auth Q]105Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q4JAJ6 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RNAP inhibitory proteinN [auth Z]149Bicaudavirus pozzuolienseMutation(s): 0 
UniProt
Find proteins for Q3V4R7 (Acidianus two-tailed virus)
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download Ideal Coordinates CCD File 
T [auth D]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
P [auth A]
Q [auth A]
R [auth A]
S [auth B]
U [auth N]
P [auth A],
Q [auth A],
R [auth A],
S [auth B],
U [auth N],
V [auth P]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.19

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom207446/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references