7Q5B | pdb_00007q5b

Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes.

Abascal-Palacios, G., Jochem, L., Pla-Prats, C., Beuron, F., Vannini, A.

(2021) Nat Commun 12: 6992-6992

  • DOI: https://doi.org/10.1038/s41467-021-27338-w
  • Primary Citation Related Structures: 
    7Q5B

  • PubMed Abstract: 

    Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity in a narrow window upstream of RNA Polymerase (Pol) III-transcribed genes, representing a paradigm for harmless targeted integration. Here we present the cryo-EM reconstruction at 4.0 Å of an active Ty3 strand transfer complex bound to TFIIIB transcription factor and a tRNA gene. The structure unravels the molecular mechanisms underlying Ty3 targeting specificity at Pol III-transcribed genes and sheds light into the architecture of retrotransposon machinery during integration. Ty3 intasome contacts a region of TBP, a subunit of TFIIIB, which is blocked by NC2 transcription regulator in RNA Pol II-transcribed genes. A newly-identified chromodomain on Ty3 integrase interacts with TFIIIB and the tRNA gene, defining with extreme precision the integration site position.

    • Organizational Affiliation: 
    • Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK. guiller.abascalpalacios@icr.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 927.78 kDa 
  • Atom Count: 21,746 
  • Modeled Residue Count: 2,423 
  • Deposited Residue Count: 7,786 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Transposon Ty3-G Gag-Pol polyproteinE [auth A],
F [auth B],
G [auth C],
H [auth D]		1,547Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99315 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q99315
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UniProt GroupQ99315
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription factor TFIIIB component B''I [auth X]594Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P46678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP46678
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
TATA-box-binding proteinJ [auth Y]240Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP13393
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription factor IIIB 70 kDa subunitK [auth Z]596Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRF1, PCF4, TDS4, YGR246C
UniProt
Find proteins for P29056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29056 
Go to UniProtKB:  P29056
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UniProt GroupP29056
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (56-MER)A [auth R]56Saccharomyces cerevisiae S288C
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (31-MER)B [auth S]31Saccharomyces cerevisiae S288C
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (34-MER)C [auth r]34Saccharomyces cerevisiae S288C
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (9-MER)D [auth s]9Saccharomyces cerevisiae S288C
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (19-MER)L [auth t],
M [auth u]		19Saccharomyces cerevisiae S288C
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomCR-UK C47547/A21536
Wellcome TrustUnited Kingdom200818/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary