6RI5

Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.

Kargas, V.Castro-Hartmann, P.Escudero-Urquijo, N.Dent, K.Hilcenko, C.Sailer, C.Zisser, G.Marques-Carvalho, M.J.Pellegrino, S.Wawiorka, L.Freund, S.M.Wagstaff, J.L.Andreeva, A.Faille, A.Chen, E.Stengel, F.Bergler, H.Warren, A.J.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.44904
  • Primary Citation of Related Structures:  
    6QIK, 6QT0, 6QTZ, 6RI5, 6RZZ, 6S05

  • PubMed Abstract: 

    During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-A254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX45 
Go to UniProtKB:  P0CX45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX45
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3387Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14126 
Go to UniProtKB:  P14126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14126
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-A256Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17076 
Go to UniProtKB:  P17076
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17076
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-BI [auth J]198Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26785 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26785 
Go to UniProtKB:  P26785
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26785
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28M [auth N]149Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02406 
Go to UniProtKB:  P02406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02406
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AP [auth Q]186Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX49 
Go to UniProtKB:  P0CX49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX49
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AU [auth V]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05749 
Go to UniProtKB:  P05749
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05749
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AW [auth X]127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05743 
Go to UniProtKB:  P05743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29Z [auth a]59Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05747 
Go to UniProtKB:  P05747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05747
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32DA [auth e]130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38061 
Go to UniProtKB:  P38061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38061
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AHA [auth i]88Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49166 
Go to UniProtKB:  P49166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49166
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BloodwiseUnited Kingdom12048
Medical Research Council (United Kingdom)United Kingdom105161083

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references, Refinement description