9N7A | pdb_00009n7a

SSU processome maturation and disassembly, State N

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2025-02-05 Released: 2025-11-05 
  • Deposition Author(s): Buzovetsky, O., Klinge, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Chan Zuckerberg Initiative

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 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

Helicase-mediated mechanism of SSU processome maturation and disassembly.

Buzovetsky, O.Klinge, S.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09688-3
  • Primary Citation of Related Structures:  
    9N6V, 9N6W, 9N6X, 9N6Y, 9N6Z, 9N70, 9N73, 9N74, 9N75, 9N76, 9N77, 9N7A

  • PubMed Abstract: 

    Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms of SSU processome maturation, remodelling, disassembly and RNA quality control, and the transitions between states remain unknown owing to a paucity of intermediates 1-3 . Here we report 16 native SSU processome structures alongside genetic data, revealing how two helicases, the Mtr4-exosome and Dhr1, are controlled for accurate and unidirectional ribosome biogenesis. Our data show how irreversible pre-ribosomal RNA degradation by the redundantly tethered RNA exosome couples the transformation of the SSU processome into a pre-40S particle, during which Utp14 can probe evolving surfaces, ultimately positioning and activating Dhr1 to unwind the U3 snoRNA and initiate nucleolar pre-40S release. This study highlights a paradigm for large dynamic RNA-protein complexes in which irreversible RNA degradation drives compositional changes and communicates these changes to govern enzyme activity while maintaining overall quality control.


  • Organizational Affiliation
    • Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AC [auth L3]146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AD [auth L4]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5E [auth L5]225Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AF [auth L6]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AG [auth L7]190Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AH [auth L8]200Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AI [auth L9]197Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AJ [auth LC]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AK [auth LD]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AL [auth LE]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AM [auth LF]135Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AN [auth LG]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10P [auth NA]593Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10Q [auth NB]610Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13R [auth NF]151Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AS [auth NG]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferaseT [auth NL]318Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.183
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1AU [auth NM]255Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AV [auth NP]144Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AW [auth NQ]82Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DHR1X [auth NS]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AY [auth NW]108Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9Z [auth SG]573Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinAA [auth SH]367Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1BA [auth SI]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.5
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1CA [auth SJ],
DA [auth SK]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1EA [auth SL]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4FA [auth SM]290Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20GA [auth SP]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AHA [auth SR]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14IA [auth SS]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14JA [auth ST]810Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4KA [auth SU]552Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1LA [auth SW]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1MA [auth SZ]483Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth L1]1,803Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
U3 snoRNAB [auth L2]334Saccharomyces cerevisiae S288C
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Entity ID: 15
MoleculeChains LengthOrganismImage
U3snoRNA segmentO [auth N2]5Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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IC [auth SI]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
HC [auth NQ],
KC [auth SL]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth L1]
AC [auth L1]
BB [auth L1]
BC [auth L1]
CB [auth L1]
AB [auth L1],
AC [auth L1],
BB [auth L1],
BC [auth L1],
CB [auth L1],
CC [auth L1],
DB [auth L1],
DC [auth L1],
EB [auth L1],
EC [auth L1],
FB [auth L1],
FC [auth L1],
GB [auth L1],
GC [auth L1],
HB [auth L1],
IB [auth L1],
JB [auth L1],
JC [auth SI],
KB [auth L1],
LB [auth L1],
MB [auth L1],
NA [auth L1],
NB [auth L1],
OA [auth L1],
OB [auth L1],
PA [auth L1],
PB [auth L1],
QA [auth L1],
QB [auth L1],
RA [auth L1],
RB [auth L1],
SA [auth L1],
SB [auth L1],
TA [auth L1],
TB [auth L1],
UA [auth L1],
UB [auth L1],
VA [auth L1],
VB [auth L1],
WA [auth L1],
WB [auth L1],
XA [auth L1],
XB [auth L1],
YA [auth L1],
YB [auth L1],
ZA [auth L1],
ZB [auth L1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
IA [auth SS]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM145950-03
Chan Zuckerberg InitiativeUnited States2023-332391

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references