8CBJ

Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex


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 1.1 of the entry. See complete history


Literature

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.

Ikeuchi, K.Ivic, N.Buschauer, R.Cheng, J.Frohlich, T.Matsuo, Y.Berninghausen, O.Inada, T.Becker, T.Beckmann, R.

(2023) Nat Commun 14: 2730-2730

  • DOI: https://doi.org/10.1038/s41467-023-38161-w
  • Primary Citation of Related Structures:  
    8C83, 8CAH, 8CAS, 8CBJ

  • PubMed Abstract: 

    In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.


  • Organizational Affiliation

    Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AA [auth b]82Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AB [auth c]67Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPS29A isoform 1C [auth d]56Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AD [auth e]63Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinE [auth g]319Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1F [auth h]274Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ENP1 isoform 1G [auth i]483Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
LTV1 isoform 1H [auth j]463Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
TSR1 isoform 1I [auth k]788Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinaseJ [auth l]425Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 2.7.11.1
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AK [auth A]252Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AL [auth B]255Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2M [auth C]254Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3N [auth D]240Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-BO [auth E]261Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5P [auth F]225Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-BQ [auth G]236Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AR [auth H]190Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AS [auth I]200Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AT [auth J]197Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AU [auth L]156Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12V [auth M]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13W [auth N]151Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AX [auth O]137Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RPS15 isoform 1Y [auth P]142Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AZ [auth Q]143Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AAA [auth R]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-ABA [auth S]146Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-ACA [auth T]144Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20DA [auth U]121Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AEA [auth V]87Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AFA [auth W]130Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AGA [auth X]145Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AHA [auth Y]135Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AIA [auth Z]108Saccharomyces cerevisiae W303Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
20S-pre-rRNA D-site endonuclease NOB1JA [auth a]459Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 3.1
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA adenine N(6)-methyltransferaseKA [auth y]318Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 2.1.1.183
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
OTU domain-containing protein 2MA [auth K]307Saccharomyces cerevisiae W303Mutation(s): 1 
Gene Names: OTU2YHL013C
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Entity ID: 38
MoleculeChains LengthOrganismImage
20S pre-ribosomal RNALA [auth 2]2,012Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NA [auth b],
OA [auth d]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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],
GC [auth 2],
HB [auth 2],
HC [auth 2],
IB [auth 2],
IC [auth 2],
JB [auth 2],
KB [auth 2],
LB [auth 2],
MB [auth 2],
NB [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
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
German Research Foundation (DFG)GermanySFB/TRR-174
German Research Foundation (DFG)GermanyBE1814/15-1
German Research Foundation (DFG)GermanyBE1814/1-1
Japan Society for the Promotion of Science (JSPS)JapanJSPS Overseas Research Fellowships
Boehringer Ingelheim Fonds (BIF)GermanyPhD fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Other