7MQ9

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

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 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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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]699Homo 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
U3 small nucleolar RNA-associated protein 4 homologU [auth LN]686Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141076 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2 homologV [auth LO]919Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241945 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6 homologW [auth LP]597Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108651 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 3X [auth LQ]943Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000065183 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18 homologY [auth LS]556Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000011260 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 36Z [auth LT]951Homo sapiensMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 13AA [auth LU]445Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164934 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 46BA [auth LW]610Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000227057 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3CA [auth LZ]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177971 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein MPP10DA [auth NA]681Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124383 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10EA [auth NB]479Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132467 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 7FA [auth ND]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000225921 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C1orf131GA [auth NE]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143633 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13HA [auth NF]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14IA [auth NG]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseJA [auth NJ],
SB [auth NK]
1,025Homo sapiensMutation(s): 0 
EC: 2.3.1
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GTEx:  ENSG00000135372 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aKA [auth NM]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AATFLA [auth NN]560Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000275700 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aMA [auth NO]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27NA [auth NQ]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
RRP12-like proteinOA [auth NR]861Homo sapiensMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aPA [auth NT]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17QA [auth NU]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 10RA [auth NW]688Homo sapiensMutation(s): 0 
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Find proteins for Q9BSC4 (Homo sapiens)
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GTEx:  ENSG00000115761 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56594Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101361 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58TA [auth SB]529Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055044 
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UniProt GroupQ9Y2X3
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinUA [auth SC],
VA [auth SD]
321Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000105202 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1WA [auth SE],
XA [auth SF]
128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinYA [auth SH]373Homo sapiensMutation(s): 0 
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PHAROS:  Q9Y2P8
GTEx:  ENSG00000120158 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1 homologZA [auth SI]1,282Homo sapiensMutation(s): 0 
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PHAROS:  Q14692
GTEx:  ENSG00000165733 
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UniProt GroupQ14692
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1AB [auth SK],
VB [auth SJ]
244Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000126749 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1 homologBB [auth SL]198Homo sapiensMutation(s): 0 
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PHAROS:  Q9Y324
GTEx:  ENSG00000119616 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4CB [auth SM]291Homo sapiensMutation(s): 0 
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PHAROS:  Q96G21
GTEx:  ENSG00000136718 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxynucleotidyltransferase terminal-interacting protein 2DB [auth SQ]756Homo sapiensMutation(s): 0 
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Find proteins for Q5QJE6 (Homo sapiens)
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PHAROS:  Q5QJE6
GTEx:  ENSG00000067334 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23EB [auth SR]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14 homolog AFB [auth SS]771Homo sapiensMutation(s): 0 
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Find proteins for Q9BVJ6 (Homo sapiens)
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GTEx:  ENSG00000156697 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned peptidesGB [auth SX]177Homo sapiensMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Probable U3 small nucleolar RNA-associated protein 11HB [auth SY]253Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3A2 (Homo sapiens)
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GTEx:  ENSG00000183520 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 6IB [auth NH]1,146Homo sapiensMutation(s): 0 
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PHAROS:  Q9H6R4
GTEx:  ENSG00000165271 
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UniProt GroupQ9H6R4
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Small subunit processome component 20 homologJB [auth SP]2,785Homo sapiensMutation(s): 0 
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PHAROS:  O75691
GTEx:  ENSG00000120800 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Transducin beta-like protein 3KB [auth LR]808Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183751 
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UniProt GroupQ12788
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT repeat-containing protein 1LB [auth LM]2,144Homo sapiensMutation(s): 0 
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Find proteins for Q9H583 (Homo sapiens)
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PHAROS:  Q9H583
GTEx:  ENSG00000119285 
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UniProt GroupQ9H583
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