5JCS

CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling

Barrio-Garcia, C.Thoms, M.Flemming, D.Kater, L.Berninghausen, O.Bassler, J.Beckmann, R.Hurt, E.

(2016) Nat Struct Mol Biol 23: 37-44

  • DOI: https://doi.org/10.1038/nsmb.3132
  • Primary Citation of Related Structures:  
    5JCS

  • PubMed Abstract: 

    Ribosome synthesis is catalyzed by ∼200 assembly factors, which facilitate efficient production of mature ribosomes. Here, we determined the cryo-EM structure of a Saccharomyces cerevisiae nucleoplasmic pre-60S particle containing the dynein-related 550-kDa Rea1 AAA(+) ATPase and the Rix1 subcomplex. This particle differs from its preceding state, the early Arx1 particle, by two massive structural rearrangements: an ∼180° rotation of the 5S ribonucleoprotein complex and the central protuberance (CP) rRNA helices, and the removal of the 'foot' structure from the 3' end of the 5.8S rRNA. Progression from the Arx1 to the Rix1 particle was blocked by mutational perturbation of the Rix1-Rea1 interaction but not by a dominant-lethal Rea1 AAA(+) ATPase-ring mutant. After remodeling, the Rix1 subcomplex and Rea1 become suitably positioned to sense correct structural maturation of the CP, which allows unidirectional progression toward mature ribosomes.


  • Organizational Affiliation

    Gene Center, University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-A254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30B [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3C [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AD [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AE [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32F [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AH [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AI [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AJ [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AK [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AL [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AM [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AN [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AO [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AP [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L1-AQ [auth I]217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL1ASSM1SSM1AYPL220W
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38R [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AS [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39T [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12-AU [auth K]165Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL12ARPL15BYEL054C
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6V [auth m]245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AW [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4X [auth n]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MRT4YKL009WYKL160
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AY [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1Z [auth o]647Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOG1YPL093WLPG15W
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AAA [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-ABA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-ACA [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly protein 4DA [auth q]515Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA4YCR072CYCR72C
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AEA [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SDA1FA [auth r]767Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SDA1YGR245C
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AGA [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
MidasinHA [auth s]4,910Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MDN1REA1YLR106CL2901L8004.13
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AIA [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24JA [auth t]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RLP24YLR009W
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AKA [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Probable metalloprotease ARX1LA [auth u]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1YDR101CYD8557.10c
EC: 3
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AMA [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AOA [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AQA [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
UniProt
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CX41
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25SA [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ATA [auth Y]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AUA [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28VA [auth a]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP02406
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Entity ID: 40
MoleculeChains LengthOrganismImage
25S ribosomal RNANA [auth x]3,396Saccharomyces cerevisiae
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Entity ID: 42
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAPA [auth y]158Saccharomyces cerevisiae
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Entity ID: 44
MoleculeChains LengthOrganismImage
5S ribosomal RNARA [auth z]121Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Other
  • Version 1.2: 2017-05-03
    Changes: Database references
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2023-02-15
    Changes: Database references