6OIG

Subunit joining exposes nascent pre-40S rRNA for processing and quality control


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7.

Rai, J.Parker, M.D.Huang, H.Choy, S.Ghalei, H.Johnson, M.C.Karbstein, K.Stroupe, M.E.

(2021) RNA 27: 221-233

  • DOI: https://doi.org/10.1261/rna.077610.120
  • Primary Citation of Related Structures:  
    6OIG, 6WDR

  • PubMed Abstract: 

    During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly intermediates are essential for maturation and quality control, how they form, and how their structure promotes quality control, remains unknown. To address these questions, we determined the structure of an 80S-like ribosome assembly intermediate to an overall resolution of 3.4 Å. The structure, validated by biochemical data, resolves a large body of previously paradoxical data and illustrates how assembly and translation factors cooperate to promote the formation of an interface that lacks many mature subunit contacts but is stabilized by the universally conserved methyltransferase Dim1. We also show how Tsr1 enables this interface by blocking the canonical binding of eIF5B to 40S subunits, while maintaining its binding to 60S. The structure also shows how this interface leads to unfolding of the platform, which allows for temporal regulation of the ATPase Fap7, thus linking 40S maturation to quality control during ribosome assembly.


  • Organizational Affiliation

    Department of Biological Science and the Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L1-AA [auth z]204Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL1ASSM1SSM1AYPL220W
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AB [auth A]252Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3C [auth B]386Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AD [auth C]361Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5E [auth D]296Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AF [auth E]175Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AG [auth F]222Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AH [auth G]233Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AI [auth H]191Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10J [auth I]220Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BK [auth J]169Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12-AL [auth s]155Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL12ARPL15BYEL054C
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AM [auth L]193Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AN [auth M]136Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AO [auth N]203Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AP [auth O]197Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AQ [auth P]183Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AR [auth Q]185Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AS [auth R]188Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AT [auth S]172Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AU [auth T]159Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AV [auth U]100Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AW [auth V]136Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AX [auth W]135Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25Y [auth X]121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AZ [auth Y]126Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AAA [auth Z]135Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28BA [auth a]148Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29CA [auth b]58Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30DA [auth c]97Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AEA [auth d]109Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32FA [auth e]127Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AGA [auth f]106Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AHA [auth g]112Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AIA [auth h]119Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AJA [auth i]99Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AKA [auth j]87Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38LA [auth k]77Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39MA [auth l]50Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40NA [auth m]52Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AOA [auth o]105Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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UniProt GroupP0CX27
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-APA [auth p]91Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX25 
Go to UniProtKB:  P0CX25
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UniProt GroupP0CX25
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0,60S acidic ribosomal protein P0,AO, L1OEQA [auth q]219Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
UniProt
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05317 
Go to UniProtKB:  P05317
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UniProt GroupP05317
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
P1UA [auth x]47Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
P2VA [auth y]46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains LengthOrganismImage
25S ribosomal RNARA [auth 5]3,394Saccharomyces cerevisiae
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Entity ID: 45
MoleculeChains LengthOrganismImage
5.8S ribosomal RNASA [auth 8]158Saccharomyces cerevisiae
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Entity ID: 46
MoleculeChains LengthOrganismImage
5S ribosomal RNATA [auth 7]121Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States55108536
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM117093
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM086451

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references