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: https://doi.org/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 of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation ...

    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-AA [auth b]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
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40S ribosomal protein S28-AB [auth c]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
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Entity ID: 3
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40S ribosomal protein S29-AC [auth d]56Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29A, RPS36A, YS29A, YLR388W, L8084.11
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Entity ID: 4
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40S ribosomal protein S30-AD [auth e]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
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Guanine nucleotide-binding protein subunit beta-like proteinE [auth g]319Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1, CPC2, YMR116C, YM9718.15C
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Entity ID: 6
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Pre-rRNA-processing protein PNO1F [auth h]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1, DIM2, RRP20, YOR145C, O3513, YOR3513C
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Entity ID: 7
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Essential nuclear protein 1G [auth i]483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1, MEG1, YBR247C, YBR1635
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LTV1H [auth j]463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LTV1, YKL143W, YKL2
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Entity ID: 9
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Ribosome biogenesis protein TSR1I [auth k]788Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TSR1, YDL060W
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Serine/threonine-protein kinase RIO2J [auth l]425Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIO2, YNL207W, N1342
EC: 2.7.11.1
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40S ribosomal protein S0-AL [auth A]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0A, NAB1, NAB1A, YST1, YGR214W
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40S ribosomal protein S1-AM [auth B]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
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40S ribosomal protein S2N [auth C]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2, RPS4, SUP38, SUP44, YGL123W, G2893
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40S ribosomal protein S3O [auth D]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3, SUF14, YNL178W, N1653
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Entity ID: 16
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40S ribosomal protein S4-AP [auth E]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
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40S ribosomal protein S5Q [auth F]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
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40S ribosomal protein S6-AR [auth G]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
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40S ribosomal protein S7-AS [auth H]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
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40S ribosomal protein S8-AT [auth I]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
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40S ribosomal protein S9-AU [auth J]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
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40S ribosomal protein S11-AV [auth L]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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40S ribosomal protein S12W [auth M]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
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40S ribosomal protein S13X [auth N]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
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40S ribosomal protein S14-AY [auth O]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14A, CRY1, RPL59, YCR031C, YCR31C
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40S ribosomal protein S15Z [auth P]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15, RPS21, YOL040C
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40S ribosomal protein S16-AAA [auth Q]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
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40S ribosomal protein S17-ABA [auth R]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17A, RP51A, YML024W
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40S ribosomal protein S18-ACA [auth S]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18A, YDR450W, D9461.35
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40S ribosomal protein S19-ADA [auth T]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19A, RP55A, RPS16AA, YOL121C
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40S ribosomal protein S20EA [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20, URP2, YHL015W
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40S ribosomal protein S21-AFA [auth V]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
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40S ribosomal protein S22-AGA [auth W]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22A, RPS24, RPS24A, YJL190C, J0355
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40S ribosomal protein S23-AHA [auth X]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
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40S ribosomal protein S24-AIA [auth Y]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
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40S ribosomal protein S25-AJA [auth Z]108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25A, RPS31A, YGR027C
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MoleculeChainsLengthOrganismImage
20S ribosomal RNAK [auth 2]1,800Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
KA [auth b],
LA [auth d]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth 2],
AC [auth 2],
BB [auth 2],
BC [auth 2],
CB [auth 2],
AB [auth 2],
AC [auth 2],
BB [auth 2],
BC [auth 2],
CB [auth 2],
CC [auth 2],
DB [auth 2],
DC [auth 2],
EB [auth 2],
EC [auth 2],
FB [auth 2],
FC [auth 2],
GB [auth 2],
HB [auth 2],
IB [auth 2],
JB [auth 2],
KB [auth 2],
LB [auth 2],
MA [auth 2],
MB [auth 2],
NA [auth 2],
NB [auth 2],
OA [auth 2],
OB [auth 2],
PA [auth 2],
PB [auth 2],
QA [auth 2],
QB [auth 2],
RA [auth 2],
RB [auth 2],
SA [auth 2],
SB [auth 2],
TA [auth 2],
TB [auth 2],
UA [auth 2],
UB [auth 2],
VA [auth 2],
VB [auth 2],
WA [auth 2],
WB [auth 2],
XA [auth 2],
XB [auth 2],
YA [auth 2],
YB [auth 2],
ZA [auth 2],
ZB [auth 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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2
MODEL REFINEMENTPHENIX1.9

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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