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- PDB-7mqa: Cryo-EM structure of the human SSU processome, state post-A1 -

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Entry
Database: PDB / ID: 7mqa
TitleCryo-EM structure of the human SSU processome, state post-A1
Components
  • (40S ribosomal protein ...) x 20
  • (Nucleolar protein ...) x 6
  • (U3 small nucleolar RNA-associated protein ...) x 5
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • (WD repeat-containing protein ...) x 5
  • 18S rRNA
  • 5'ETS rRNA
  • Active regulator of SIRT1
  • Bystin
  • DDB1- and CUL4-associated factor 13
  • Deoxynucleotidyltransferase terminal-interacting protein 2
  • Exosome component 10
  • HEAT repeat-containing protein 1
  • NHP2-like protein 1
  • Nucleolar complex protein 4 homolog
  • Periodic tryptophan protein 2 homolog
  • Probable ATP-dependent RNA helicase DHX37
  • Probable U3 small nucleolar RNA-associated protein 11
  • Probable dimethyladenosine transferase
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA-binding protein PNO1
  • RRP12-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Ribosomal RNA-processing protein 7 homolog A
  • Ribosome biogenesis protein BMS1 homolog
  • Small subunit processome component 20 homolog
  • Something about silencing protein 10
  • Transducin beta-like protein 3
  • U3 small nucleolar RNA-interacting protein 2
  • U3 snoRNA
  • Ubiquitin-40S ribosomal protein S27a
  • Unassigned peptides
  • rRNA 2'-O-methyltransferase fibrillarin
  • rRNA-processing protein FCF1 homolog
KeywordsRIBOSOME / Ribosomal assembly intermediate
Function / homology
Function and homology information


U6 snRNA 2'-O-ribose methyltransferase activity / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / positive regulation of mRNA cis splicing, via spliceosome / snoRNA localization / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process ...U6 snRNA 2'-O-ribose methyltransferase activity / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / positive regulation of mRNA cis splicing, via spliceosome / snoRNA localization / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / granular component / RNA exonuclease activity / nuclear polyadenylation-dependent CUT catabolic process / regulation of telomerase RNA localization to Cajal body / positive regulation of male gonad development / U4atac snRNP / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / CURI complex / UTP-C complex / CUT catabolic process / regulation of stem cell population maintenance / cytoplasmic exosome (RNase complex) / t-UTP complex / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / U4atac snRNA binding / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / nuclear exosome (RNase complex) / rRNA (pseudouridine) methyltransferase activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-snoRNP complex / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA binding / preribosome / rRNA (adenine-N6,N6-)-dimethyltransferase activity / histone mRNA catabolic process / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / dense fibrillar component / histone methyltransferase binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription elongation by RNA polymerase II / box C/D methylation guide snoRNP complex / positive regulation of rRNA processing / tRNA export from nucleus / cilium disassembly / rRNA primary transcript binding / RNA splicing, via transesterification reactions / transcription elongation factor activity / sno(s)RNA-containing ribonucleoprotein complex / spindle assembly involved in female meiosis / rRNA base methylation / blastocyst formation / U4 snRNA binding / positive regulation of respiratory burst involved in inflammatory response / protein localization to nucleolus / epigenetic programming in the zygotic pronuclei / nucleolus organization / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / telomerase RNA binding / rRNA methylation / negative regulation of RNA splicing / RNA catabolic process / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / box C/D snoRNP assembly / neural precursor cell proliferation / neural crest cell differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U3 snoRNA binding / negative regulation of bicellular tight junction assembly / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / precatalytic spliceosome / Cul4-RING E3 ubiquitin ligase complex / snoRNA binding / preribosome, small subunit precursor / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / rRNA metabolic process / positive regulation of transcription by RNA polymerase I / negative regulation of telomere maintenance via telomerase / fibroblast growth factor binding / Association of TriC/CCT with target proteins during biosynthesis / monocyte chemotaxis / Protein hydroxylation / TOR signaling / RNA polymerase II complex binding / SARS-CoV-1 modulates host translation machinery / decidualization
Similarity search - Function
: / DEAH helicase DHX37 C-terminal domain / Active regulator of SIRT1 / Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1 / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / : / NUC129 domain / U3 small nucleolar RNA-associated protein 6 C-terminal / WD repeat-containing protein 75 first beta-propeller ...: / DEAH helicase DHX37 C-terminal domain / Active regulator of SIRT1 / Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1 / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / : / NUC129 domain / U3 small nucleolar RNA-associated protein 6 C-terminal / WD repeat-containing protein 75 first beta-propeller / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20, C-terminal / : / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20 domain / Small subunit processome component 20 homolog, C-terminal / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 4 / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / rRNA-processing protein Fcf1, PIN domain / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / : / : / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / BING4CT (NUC141) domain / : / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 15, C-terminal / Utp14 protein / UTP15 C terminal / rRNA-processing protein Fcf1/Utp23 / Sas10 C-terminal domain / Fcf1 / Sas10 C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / : / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / : / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / HEATR1-like, HEAT repeats / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Sas10/Utp3/C1D / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / Utp21 specific WD40 associated putative domain / WDR36/Utp21 second beta-propeller domain / WDR36/Utp21 first beta-propeller / Ribosomal RNA-processing protein Rrp9-like / Helicase and RNase D C-terminal / HRDC domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / U3 small nucleolar ribonucleoprotein protein MPP10 / Nucleolar protein 56 / WD repeat-containing protein 46 / U3 small nucleolar RNA-interacting protein 2 / Small subunit processome component 20 homolog / Small ribosomal subunit protein eS17 / rRNA 2'-O-methyltransferase fibrillarin / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / NHP2-like protein 1 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Exosome complex component 10 / Transducin beta-like protein 3 / Ribosome biogenesis protein BMS1 homolog / WD repeat-containing protein 43 / Periodic tryptophan protein 2 homolog / Deoxynucleotidyltransferase terminal-interacting protein 2 / Active regulator of SIRT1 / WD repeat-containing protein 75 / Probable ATP-dependent RNA helicase DHX37 / WD repeat-containing protein 36 / U3 small nucleolar RNA-associated protein 15 homolog / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 4 homolog / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 14 homolog A / HEAT repeat-containing protein 1 / Nucleolar protein 6 / Something about silencing protein 10 / RNA-binding protein PNO1 / DDB1- and CUL4-associated factor 13 / U3 small nucleolar ribonucleoprotein protein IMP3 / U3 small nucleolar RNA-associated protein 6 homolog / U3 small nucleolar RNA-associated protein NOL7 / Dimethyladenosine transferase / WD repeat-containing protein 3 / RNA 3'-terminal phosphate cyclase-like protein / Nucleolar protein 58 / rRNA-processing protein FCF1 homolog / Probable U3 small nucleolar RNA-associated protein 11 / Ribosomal RNA-processing protein 7 homolog A / U3 small nucleolar RNA-associated protein 18 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsVanden Broeck, A. / Singh, S. / Klinge, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
European Molecular Biology Organization (EMBO)ALTF 711-2019
CitationJournal: Science / Year: 2021
Title: Nucleolar maturation of the human small subunit processome.
Authors: Sameer Singh / Arnaud Vanden Broeck / Linamarie Miller / Malik Chaker-Margot / Sebastian Klinge /
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 ...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.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
L0: 5'ETS rRNA
L1: 18S rRNA
L2: U3 snoRNA
L3: 40S ribosomal protein S18
L4: 40S ribosomal protein S4, X isoform
L5: 40S ribosomal protein S5
L6: 40S ribosomal protein S6
L7: 40S ribosomal protein S7
L8: 40S ribosomal protein S8
L9: 40S ribosomal protein S9
LA: 40S ribosomal protein S12
LC: 40S ribosomal protein S16
LD: 40S ribosomal protein S11
LF: 40S ribosomal protein S24
LG: 40S ribosomal protein S28
LH: WD repeat-containing protein 75
LI: Nucleolar protein 11
LJ: U3 small nucleolar RNA-associated protein 15 homolog
LK: WD repeat-containing protein 43
LL: WD repeat-containing protein 43
LM: HEAT repeat-containing protein 1
LN: U3 small nucleolar RNA-associated protein 4 homolog
LO: Periodic tryptophan protein 2 homolog
LP: U3 small nucleolar RNA-associated protein 6 homolog
LQ: WD repeat-containing protein 3
LR: Transducin beta-like protein 3
LS: U3 small nucleolar RNA-associated protein 18 homolog
LT: WD repeat-containing protein 36
LU: DDB1- and CUL4-associated factor 13
LW: WD repeat-containing protein 46
LY: Active regulator of SIRT1
LZ: U3 small nucleolar ribonucleoprotein protein IMP3
NA: U3 small nucleolar ribonucleoprotein protein MPP10
NB: Something about silencing protein 10
ND: Nucleolar protein 7
NF: 40S ribosomal protein S13
NG: 40S ribosomal protein S14
NH: Nucleolar protein 6
NI: Ribosomal RNA-processing protein 7 homolog A
NL: Probable dimethyladenosine transferase
NM: 40S ribosomal protein S3a
NO: 40S ribosomal protein S15a
NP: 40S ribosomal protein S19
NQ: 40S ribosomal protein S27
NR: RRP12-like protein
NS: Probable ATP-dependent RNA helicase DHX37
NT: Ubiquitin-40S ribosomal protein S27a
NU: 40S ribosomal protein S17
NV: Exosome component 10
SA: Nucleolar protein 56
SB: Nucleolar protein 58
SC: rRNA 2'-O-methyltransferase fibrillarin
SD: rRNA 2'-O-methyltransferase fibrillarin
SE: NHP2-like protein 1
SF: NHP2-like protein 1
SG: U3 small nucleolar RNA-interacting protein 2
SH: RNA 3'-terminal phosphate cyclase-like protein
SI: Ribosome biogenesis protein BMS1 homolog
SJ: Ribosomal RNA small subunit methyltransferase NEP1
SK: Ribosomal RNA small subunit methyltransferase NEP1
SL: rRNA-processing protein FCF1 homolog
SM: U3 small nucleolar ribonucleoprotein protein IMP4
SP: Small subunit processome component 20 homolog
SQ: Deoxynucleotidyltransferase terminal-interacting protein 2
SR: 40S ribosomal protein S23
SS: U3 small nucleolar RNA-associated protein 14 homolog A
ST: Nucleolar protein 14
SU: Nucleolar complex protein 4 homolog
SW: RNA-binding protein PNO1
SX: Unassigned peptides
SY: Probable U3 small nucleolar RNA-associated protein 11
SZ: Bystin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,578,683143
Polymers5,575,13272
Non-polymers3,55171
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L0L1L2

#1: RNA chain 5'ETS rRNA


Mass: 1166881.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1212788588
#2: RNA chain 18S rRNA


Mass: 604234.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227
#3: RNA chain U3 snoRNA


Mass: 70017.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 37551

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40S ribosomal protein ... , 20 types, 20 molecules L3L4L5L6L7L8L9LALCLDLFLGNFNGNMNONPNQNUSR

#4: Protein 40S ribosomal protein S18


Mass: 12671.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#5: Protein 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#6: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#7: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#8: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#9: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#10: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#11: Protein 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#12: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#13: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#14: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#15: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#35: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#36: Protein 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#40: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#41: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#42: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#43: Protein 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#47: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#61: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266

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WD repeat-containing protein ... , 5 types, 6 molecules LHLKLLLQLTLW

#16: Protein WD repeat-containing protein 75 / U3 small nucleolar RNA-associated protein 17 homolog


Mass: 94609.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IWA0
#19: Protein WD repeat-containing protein 43 / U3 small nucleolar RNA-associated protein 5 homolog


Mass: 74985.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15061
#24: Protein WD repeat-containing protein 3


Mass: 106248.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNX4
#27: Protein WD repeat-containing protein 36 / T-cell activation WD repeat-containing protein / TA-WDRP


Mass: 105443.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NI36
#29: Protein WD repeat-containing protein 46 / WD repeat-containing protein BING4


Mass: 68189.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15213

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Nucleolar protein ... , 6 types, 6 molecules LINDNHSASBST

#17: Protein Nucleolar protein 11


Mass: 73444.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#34: Protein Nucleolar protein 7 / Nucleolar protein of 27 kDa


Mass: 29483.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UMY1
#37: Protein Nucleolar protein 6 / Nucleolar RNA-associated protein / Nrap


Mass: 127748.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H6R4
#49: Protein Nucleolar protein 56 / Nucleolar protein 5A


Mass: 66160.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00567
#50: Protein Nucleolar protein 58 / Nucleolar protein 5


Mass: 59686.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2X3
#63: Protein Nucleolar protein 14


Mass: 68259.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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U3 small nucleolar RNA-associated protein ... , 5 types, 5 molecules LJLNLPLSSS

#18: Protein U3 small nucleolar RNA-associated protein 15 homolog


Mass: 58503.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TED0
#21: Protein U3 small nucleolar RNA-associated protein 4 homolog / Cirhin / UTP4 small subunit processome component


Mass: 76993.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969X6
#23: Protein U3 small nucleolar RNA-associated protein 6 homolog / Hepatocellular carcinoma-associated antigen 66 / Multiple hat domains protein


Mass: 70297.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYH9
#26: Protein U3 small nucleolar RNA-associated protein 18 homolog / WD repeat-containing protein 50


Mass: 62097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5J1
#62: Protein U3 small nucleolar RNA-associated protein 14 homolog A / Antigen NY-CO-16 / Serologically defined colon cancer antigen 16


Mass: 88129.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BVJ6

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Protein , 26 types, 29 molecules LMLOLRLULYNBNINLNRNSNTNVSCSDSESFSGSHSISJSKSLSPSQSUSWSXSYSZ

#20: Protein HEAT repeat-containing protein 1 / Protein BAP28 / U3 small nucleolar RNA-associated protein 10 homolog


Mass: 242649.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H583
#22: Protein Periodic tryptophan protein 2 homolog


Mass: 102574.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15269
#25: Protein Transducin beta-like protein 3 / WD repeat-containing protein SAZD


Mass: 89143.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12788
#28: Protein DDB1- and CUL4-associated factor 13 / WD repeat and SOF domain-containing protein 1


Mass: 51489.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NV06
#30: Protein Active regulator of SIRT1 / 40S ribosomal protein S19-binding protein 1 / RPS19-binding protein 1 / S19BP


Mass: 15468.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86WX3
#33: Protein Something about silencing protein 10 / Charged amino acid-rich leucine zipper 1 / CRL1 / Disrupter of silencing SAS10 / UTP3 homolog


Mass: 54652.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NQZ2
#38: Protein Ribosomal RNA-processing protein 7 homolog A / Gastric cancer antigen Zg14


Mass: 32393.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3A4
#39: Protein Probable dimethyladenosine transferase / DIM1 dimethyladenosine transferase 1 homolog / DIM1 dimethyladenosine transferase 1-like / Probable ...DIM1 dimethyladenosine transferase 1 homolog / DIM1 dimethyladenosine transferase 1-like / Probable 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / Probable 18S rRNA dimethylase / Probable S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 35292.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UNQ2, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
#44: Protein RRP12-like protein


Mass: 73292.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#45: Protein Probable ATP-dependent RNA helicase DHX37 / DEAH box protein 37


Mass: 129727.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IY37, RNA helicase
#46: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#48: Protein Exosome component 10 / Autoantigen PM/Scl 2 / P100 polymyositis-scleroderma overlap syndrome-associated autoantigen / ...Autoantigen PM/Scl 2 / P100 polymyositis-scleroderma overlap syndrome-associated autoantigen / Polymyositis/scleroderma autoantigen 100 kDa / PM/Scl-100 / Polymyositis/scleroderma autoantigen 2


Mass: 100974.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q01780, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#51: Protein rRNA 2'-O-methyltransferase fibrillarin / 34 kDa nucleolar scleroderma antigen / Histone-glutamine methyltransferase / U6 snRNA 2'-O- ...34 kDa nucleolar scleroderma antigen / Histone-glutamine methyltransferase / U6 snRNA 2'-O-methyltransferase fibrillarin


Mass: 33843.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P22087, Transferases; Transferring one-carbon groups; Methyltransferases
#52: Protein NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 ...High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 small nuclear ribonucleoprotein SNU13 / U4/U6.U5 tri-snRNP 15.5 kDa protein


Mass: 14191.524 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#53: Protein U3 small nucleolar RNA-interacting protein 2 / RRP9 homolog / U3 small nucleolar ribonucleoprotein-associated 55 kDa protein / U3 snoRNP- ...RRP9 homolog / U3 small nucleolar ribonucleoprotein-associated 55 kDa protein / U3 snoRNP-associated 55 kDa protein / U3-55K


Mass: 51920.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43818
#54: Protein RNA 3'-terminal phosphate cyclase-like protein


Mass: 40893.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2P8
#55: Protein Ribosome biogenesis protein BMS1 homolog / Ribosome assembly protein BMS1 homolog


Mass: 146044.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14692
#56: Protein Ribosomal RNA small subunit methyltransferase NEP1 / 18S rRNA (pseudouridine(1248)-N1)-methyltransferase / 18S rRNA Psi1248 methyltransferase / ...18S rRNA (pseudouridine(1248)-N1)-methyltransferase / 18S rRNA Psi1248 methyltransferase / Nucleolar protein EMG1 homolog / Protein C2f / Ribosome biogenesis protein NEP1


Mass: 26757.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q92979, Transferases; Transferring one-carbon groups; Methyltransferases
#57: Protein rRNA-processing protein FCF1 homolog


Mass: 23416.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y324
#59: Protein Small subunit processome component 20 homolog / Down-regulated in metastasis protein / Novel nucleolar protein 73 / NNP73 / Protein Key-1A6


Mass: 318813.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75691
#60: Protein Deoxynucleotidyltransferase terminal-interacting protein 2 / Estrogen receptor-binding protein / LPTS-interacting protein 2 / LPTS-RP2 / Terminal ...Estrogen receptor-binding protein / LPTS-interacting protein 2 / LPTS-RP2 / Terminal deoxynucleotidyltransferase-interacting factor 2 / TdIF2 / TdT-interacting factor 2


Mass: 84598.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5QJE6
#64: Protein Nucleolar complex protein 4 homolog


Mass: 50184.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#65: Protein RNA-binding protein PNO1 / Partner of NOB1


Mass: 27970.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX1
#66: Protein Unassigned peptides


Mass: 19421.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#67: Protein Probable U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / UTP11-like protein


Mass: 30520.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3A2
#68: Protein Bystin


Mass: 33712.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules LZNASM

#31: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / U3 snoRNP protein IMP3 / BRMS2


Mass: 21889.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NV31
#32: Protein U3 small nucleolar ribonucleoprotein protein MPP10 / M phase phosphoprotein 10


Mass: 78988.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00566
#58: Protein U3 small nucleolar ribonucleoprotein protein IMP4 / U3 snoRNP protein IMP4 / Brix domain-containing protein 4


Mass: 33818.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96G21

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Non-polymers , 5 types, 71 molecules

#69: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: Mg
#70: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#71: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#72: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#73: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human SSU processome / Type: RIBOSOME / Entity ID: #1-#68 / Source: NATURAL
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 84904
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4Gctfv1.06CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIX1.19model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14PHENIX1.193D reconstructionphenix.combine_focused_maps
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9297626
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459775
Details: 15 focused maps were reconstructed in RELION 3.1 and then assembled into a unique composite map using phenix.combine_focused_maps. Two half maps were generated using each half map from the focused refinement.
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15WLC

5wlc

15WLC1PDBexperimental model
26ZQD

6zqd

16ZQD2PDBexperimental model
36ZOJ

6zoj

16ZOJ3PDBexperimental model
42IPX

2ipx

12IPX4PDBexperimental model
52OZB

2ozb

12OZB5PDBexperimental model
64JXM

4jxm

14JXM6PDBexperimental model
75FAI

5fai

15FAI7PDBexperimental model
86G18

6g18

16G188PDBexperimental model
96G4S

6g4s

16G4S9PDBexperimental model
106O16

6o16

16O1610PDBexperimental model
116W6C

6w6c

16W6C11PDBexperimental model

+
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