9N79 | pdb_00009n79

SSU processome maturation and disassembly, State M

  • 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: 3.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Mechanism of helicase-mediated SSU processome maturation and disassembly

Buzovetsky, O., Klinge, S.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AC [auth L3]146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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 
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AH [auth L8]200Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AI [auth L9]197Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AJ [auth LC]143Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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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 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AM [auth LF]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AN [auth LG]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10P [auth NA]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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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
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AS [auth NG]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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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 
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AV [auth NP]144Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AW [auth NQ]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for Q04217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AY [auth NW]108Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56Z [auth SA]504Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58AA [auth SB]511Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinBA [auth SC],
CA [auth SD]		327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinDA [auth SE],
EA [auth SF]		126Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9FA [auth SG]573Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinGA [auth SH]367Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1HA [auth SI]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.5
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1IA [auth SJ],
JA [auth SK]		252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
UniProt
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1KA [auth SL]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4LA [auth SM]290Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20MA [auth SP]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ANA [auth SR]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14OA [auth SS]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14PA [auth ST]810Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4QA [auth SU]552Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1RA [auth SW]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1SA [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
Download Ideal Coordinates CCD File 
OC [auth SI]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
NC [auth NQ],
QC [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],
HC [auth L1],
IB [auth L1],
IC [auth L1],
JB [auth L1],
JC [auth L1],
KB [auth L1],
KC [auth L1],
LB [auth L1],
LC [auth L1],
MB [auth L1],
MC [auth L1],
NB [auth L1],
OB [auth L1],
PB [auth L1],
PC [auth SI],
QB [auth L1],
RB [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		OA [auth SS]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.93 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