8BWS

Structure of yeast RNA Polymerase III elongation complex at 3.3 A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration.

Nguyen, P.Q.Huecas, S.Asif-Laidin, A.Plaza-Pegueroles, A.Capuzzi, B.Palmic, N.Conesa, C.Acker, J.Reguera, J.Lesage, P.Fernandez-Tornero, C.

(2023) Nat Commun 14: 1729-1729

  • DOI: https://doi.org/10.1038/s41467-023-37109-4
  • Primary Citation of Related Structures:  
    7Z0H, 7Z2Z, 7Z30, 7Z31, 8BWS

  • PubMed Abstract: 

    The yeast Ty1 retrotransposon integrates upstream of genes transcribed by RNA polymerase III (Pol III). Specificity of integration is mediated by an interaction between the Ty1 integrase (IN1) and Pol III, currently uncharacterized at the atomic level. We report cryo-EM structures of Pol III in complex with IN1, revealing a 16-residue segment at the IN1 C-terminus that contacts Pol III subunits AC40 and AC19, an interaction that we validate by in vivo mutational analysis. Binding to IN1 associates with allosteric changes in Pol III that may affect its transcriptional activity. The C-terminal domain of subunit C11, involved in RNA cleavage, inserts into the Pol III funnel pore, providing evidence for a two-metal mechanism during RNA cleavage. Additionally, ordering next to C11 of an N-terminal portion from subunit C53 may explain the connection between these subunits during termination and reinitiation. Deletion of the C53 N-terminal region leads to reduced chromatin association of Pol III and IN1, and a major fall in Ty1 integration events. Our data support a model in which IN1 binding induces a Pol III configuration that may favor its retention on chromatin, thereby improving the likelihood of Ty1 integration.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040, Madrid, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC11,460Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO31RPC1RPC160YOR116CO3254YOR3254C
EC: 2.7.7.6
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC21,149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RET1RPC128RPC2YOR207C
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1335Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC40RPC5YPR110CP8283.18
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC9161Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC17YJL011CJ1349
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC8212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC25YKL144CUNF1YKL1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC10110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC11YDR045CYD9609.01C
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC19YNL113WN1937
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC476Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC5282Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC37YKR025W
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC4422Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC53RPC4YDL150WD1557
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC3654Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC82RPC3YPR190CP9677.11
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC6317Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC34YNR003CN2031
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC7251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC31ACP2RPC8YNL151CN1769
UniProt
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Entity ID: 18
MoleculeChains LengthOrganismImage
Non-template DNAR [auth S]52Saccharomyces cerevisiae S288C
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Entity ID: 19
MoleculeChains LengthOrganismImage
Template DNAS [auth T]52Saccharomyces cerevisiae S288C
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Entity ID: 20
MoleculeChains LengthOrganismImage
RNAT [auth R]10Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4QM
Query on 4QM

Download Ideal Coordinates CCD File 
AA [auth I],
X [auth A],
Z [auth C]
(3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol
C24 H42 O3
PFZUIDNKXWIWBG-YHEMGIGTSA-N
ZN
Query on ZN

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BA [auth I]
CA [auth J]
DA [auth L]
U [auth A]
V [auth A]
BA [auth I],
CA [auth J],
DA [auth L],
U [auth A],
V [auth A],
Y [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European Union8023
Fondation ARCFranceARCDOC42020010001355
Agence Nationale de la Recherche (ANR)FranceANR-17-CE11-0025
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2017-87397-P
Spanish National Research CouncilSpain2020AEP152
European Regional Development FundEuropean UnionPID2020-116722GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection