7MQ8

Cryo-EM structure of the human SSU processome, state pre-A1

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-05-05 Released: 2021-09-22 
  • Deposition Author(s): Vanden Broeck, A., Singh, S., Klinge, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Nucleolar maturation of the human small subunit processome.

Singh, S., Vanden Broeck, A., Miller, L., Chaker-Margot, M., Klinge, S.

(2021) Science 373: eabj5338-eabj5338

  • DOI: https://doi.org/10.1126/science.abj5338
  • Primary Citation of Related Structures:  
    7MQ8, 7MQ9, 7MQA, 7MQJ

  • PubMed Abstract: 

    The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within.

    • Organizational Affiliation: 

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18D [auth L3]116Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE [auth L4]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth L5]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6G [auth L6]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7H [auth L7]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8I [auth L8]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9J [auth L9]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12K [auth LA]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16L [auth LC]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11M [auth LD]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24N [auth LF]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28O [auth LG]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 75P [auth LH]830Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115368 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 11Q [auth LI]678Homo sapiensMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15 homologR [auth LJ]518Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164338 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 43S [auth LK],
T [auth LL]		677Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163811 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT repeat-containing protein 1U [auth LM]2,144Homo sapiensMutation(s): 0 
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PHAROS:  Q9H583
GTEx:  ENSG00000119285 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4 homologV [auth LN]686Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141076 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2 homologW [auth LO]919Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241945 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6 homologX [auth LP]597Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108651 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 3Y [auth LQ]943Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000065183 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Transducin beta-like protein 3Z [auth LR]808Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183751 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18 homologAA [auth LS]556Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000011260 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 36BA [auth LT]951Homo sapiensMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 13CA [auth LU]445Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164934 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 46DA [auth LW]610Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000227057 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3EA [auth LZ]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177971 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein MPP10GA [auth NA]681Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124383 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10HA [auth NB]479Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132467 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NeuroguidinIA [auth NC]315Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129460 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 7JA [auth ND]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000225921 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C1orf131KA [auth NE]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143633 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13LA [auth NF]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14MA [auth NG]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 6NA [auth NH]1,146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165271 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7 homolog AOA [auth NI]280Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189306 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferasePA [auth NJ],
QA [auth NK]		1,025Homo sapiensMutation(s): 0 
EC: 2.3.1
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GTEx:  ENSG00000135372 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aRA [auth NM]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AATFSA [auth NN]560Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000275700 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aTA [auth NO]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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UniProt GroupP62244
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27UA [auth NQ]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
RRP12-like proteinVA [auth NR]861Homo sapiensMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aWA [auth NT]156Homo sapiensMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17XA [auth NU]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 10YA [auth NW]688Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115761 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome component homologZA [auth NY]381Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111615 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56AB [auth SA]594Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101361 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58BB [auth SB]529Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055044 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinCB [auth SC],
DB [auth SD]		321Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000105202 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1EB [auth SE],
FB [auth SF]		128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-interacting protein 2GB [auth SG]475Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114767 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinHB [auth SH]373Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120158 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1 homologIB [auth SI]1,282Homo sapiensMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1JB [auth SJ],
KB [auth SK]		244Homo sapiensMutation(s): 0 
EC: 2.1.1
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Find proteins for Q92979 (Homo sapiens)
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GTEx:  ENSG00000126749 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1 homologLB [auth SL]198Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000119616 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4MB [auth SM]291Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136718 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Small subunit processome component 20 homologNB [auth SP]2,785Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120800 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxynucleotidyltransferase terminal-interacting protein 2OB [auth SQ]756Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000067334 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23PB [auth SR]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14 homolog AQB [auth SS]771Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156697 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 14RB [auth ST]632Homo sapiensMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4 homologSB [auth SU]472Homo sapiensMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein PNO1TB [auth SW]252Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115946 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned peptideUB [auth Sx]38Homo sapiensMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned peptidesVB [auth SX]273Homo sapiensMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Probable U3 small nucleolar RNA-associated protein 11WB [auth SY]253Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183520 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
BystinXB [auth SZ]304Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'ETS rRNAA [auth L0]3,617Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth L1]1,869Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
U3 snoRNAC [auth L2]217Homo sapiens
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Entity ID: 31
MoleculeChains LengthOrganismImage
5'ETS rRNAFA [auth N0]22Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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WC [auth SI]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP
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RC [auth NH],
TC [auth NK]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SAH
Query on SAH
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YC [auth SJ],
ZC [auth SK]		S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN
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AD [auth SL],
UC [auth NQ],
VC [auth NT]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AC [auth L1]
BC [auth L1]
BD [auth SL]
CC [auth L1]
DC [auth L1]
AC [auth L1],
BC [auth L1],
BD [auth SL],
CC [auth L1],
DC [auth L1],
EC [auth L1],
FC [auth L1],
GC [auth L1],
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],
SC [auth NH],
XC [auth SI],
YB [auth L1],
ZB [auth L1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.19
MODEL REFINEMENTPHENIX1.19

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 States1DP2GM123459
European Molecular Biology Organization (EMBO)ALTF 711-2019

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-08-28
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary