6FAI

Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit.

Scaiola, A.Pena, C.Weisser, M.Bohringer, D.Leibundgut, M.Klingauf-Nerurkar, P.Gerhardy, S.Panse, V.G.Ban, N.

(2018) EMBO J 37

  • DOI: 10.15252/embj.201798499
  • Primary Citation of Related Structures:  
    6FAI

  • PubMed Abstract: 
  • Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure ...

    Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland vpanse@imm.uzh.ch ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-Ab82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-Ac67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-Ad56Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-Ae63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteing319Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1h274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LTV1j463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LTV1YKL143WYKL2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase RIO2l425Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIO2YNL207WN1342
EC: 2.7.11.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AA252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-AB255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8-AI200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-AJ197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12M143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13N151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15P142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-AQ143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-AS146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-AT144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20U121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AW130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-AX145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-AY135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-AG236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-AH190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-AL156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-AO137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-AR136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-AV87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 36
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40S ribosomal protein S25-AZ108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Essential nuclear protein 1i483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein TSR1k788Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TSR1YDL060W
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Entity ID: 11
MoleculeChainsLengthOrganismImage
20S ribosomal RNA21800Saccharomyces cerevisiae S288C
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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b, d
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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2
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references