9N6Y | pdb_00009n6y

SSU processome maturation and disassembly, State C

  • 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: 3.65 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AD [auth L3]146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE [auth L4]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth L5]225Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AG [auth L6]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AH [auth L7]190Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AI [auth L8]200Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AJ [auth L9]197Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AK [auth LC]143Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AL [auth LD]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AM [auth LE]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AN [auth LF]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AO [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
NET1-associated nuclear protein 1P [auth LH]896Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8Q [auth LI]713Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15R [auth LJ]513Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9S [auth LK]575Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5T [auth LL]643Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10U [auth LM]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4V [auth LN]776Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2W [auth LO]923Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6X [auth LP]440Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12Y [auth LQ]943Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13Z [auth LR]817Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18AA [auth LS]594Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21BA [auth LT]939Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOF1CA [auth LU]489Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2DA [auth LV]707Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7EA [auth LW]554Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseFA [auth LX],
GA [auth LY]
1,056Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.1
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3HA [auth LZ]183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10IA [auth NA]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10JA [auth NB]610Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein LCP5KA [auth NC]357Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 21LA [auth ND]214Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAF1MA [auth NE]346Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13NA [auth NF]151Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AOA [auth NG]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22PA [auth NH]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7QA [auth NI]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentRA [auth NK]316Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1ASA [auth NM]255Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BFR2TA [auth NN]534Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AUA [auth NQ]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6VA [auth NV]733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA biogenesis protein RRP5WA [auth OA]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56XA [auth SA]504Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58YA [auth SB]511Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinAB [auth SD],
ZA [auth SC]
327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinBB [auth SE],
CB [auth SF]
126Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9DB [auth SG]573Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinEB [auth SH]367Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1FB [auth SI]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.5
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Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1GB [auth SJ],
HB [auth SK]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
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Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1IB [auth SL]189Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4JB [auth SM]290Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P53941 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein UTP30KB [auth SN]274Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20LB [auth SP]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF2MB [auth SQ]217Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ANB [auth SR]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14OB [auth SS]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14PB [auth ST]810Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4QB [auth SU]552Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of rDNA transcription protein 14RB [auth SV]206Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1SB [auth SW]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11TB [auth SY]250Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1UB [auth SZ]483Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'ETS rRNAA [auth L0]700Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth L1]1,808Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChains LengthOrganismImage
TPA: Saccharomyces cerevisiae U3a gene for small nucleolar RNA U3aC [auth L2]333Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

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AD [auth NH]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN

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CD [auth NQ],
FD [auth SL]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth L1]
BC [auth L1]
BD [auth NH]
CC [auth L1]
DC [auth L1]
AC [auth L1],
BC [auth L1],
BD [auth NH],
CC [auth L1],
DC [auth L1],
EC [auth L1],
ED [auth SI],
FC [auth L1],
GC [auth L1],
GD [auth SM],
HC [auth L1],
IC [auth L1],
JC [auth L1],
KC [auth L1],
LC [auth L1],
MC [auth L1],
NC [auth L1],
OC [auth L1],
PC [auth L1],
QC [auth L1],
RC [auth L1],
SC [auth L1],
TC [auth L1],
UC [auth L1],
VB [auth L0],
VC [auth L1],
WB [auth L0],
WC [auth L1],
XB [auth L0],
XC [auth L1],
YB [auth L1],
YC [auth L2],
ZB [auth L1],
ZC [auth L2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
W [auth LO]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 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