6RBE

State 2 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles


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 1.3 of the entry. See complete history


Literature

Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism.

Mitterer, V.Shayan, R.Ferreira-Cerca, S.Murat, G.Enne, T.Rinaldi, D.Weigl, S.Omanic, H.Gleizes, P.E.Kressler, D.Plisson-Chastang, C.Pertschy, B.

(2019) Nat Commun 10: 2754-2754

  • DOI: 10.1038/s41467-019-10678-z
  • Primary Citation of Related Structures:  
    6RBE, 6RBD

  • PubMed Abstract: 
  • Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit ...

    Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps.


    Organizational Affiliation

    Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria. brigitte.pertschy@uni-graz.at.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth A]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-AC [auth B]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth C]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-AF [auth G]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-AG [auth H]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8-AH [auth I]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-AI [auth J]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-AJ [auth L]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13K [auth N]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-AL [auth O]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-AM [auth R]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-AN [auth V]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AO [auth W]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-AP [auth X]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-AQ [auth Y]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-AR [auth b]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-AS [auth d]56Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-AT [auth e]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3U [auth D]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5V [auth F]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10-AW [auth K]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12X [auth M]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15Y [auth P]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-AZ [auth Q]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-AAA [auth S]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-ABA [auth T]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20CA [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-ADA [auth Z]108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-AEA [auth c]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31FA [auth f]152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinGA [auth g]319Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth 2]1800Saccharomyces cerevisiae S288C
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
French National Research AgencyFranceRIBOMAN

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2020-01-22
    Changes: Database references