6QTZ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

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: 10.7554/eLife.44904
  • Structures With Same Primary Citation

  • 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 o ...

    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

    Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AB254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3C387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AD362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-AE174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AF191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AH256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-BJ198Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-AL137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28N149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AO204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-AR189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-AS172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-AT160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AU184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25W142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-AX127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-AY136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29a59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-Ab244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30c105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32e130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-Af107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-Ag121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-Ah100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38j78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-Al106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-Am92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic 60S subunit biogenesis factor REH1z432Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal export protein NMD3w518Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
uL1p210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10q221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40t128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AK199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AM138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5P297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-AQ186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-AV121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-AZ120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-Ad113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-Ai88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39k51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6n245Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-Av155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Large subunit GTPase 1o640Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AG176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
25S rRNAA3396Saccharomyces cerevisiae

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Entity ID: 47
MoleculeChainsLengthOrganism
5S rRNAx121Saccharomyces cerevisiae

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Entity ID: 48
MoleculeChainsLengthOrganism
5.8S rRNAy158Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
g, i, l, m, t, w
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references