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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 ...Nucleolus) x 6
  • (U3 small nucleolar RNA-associated protein ...) x 5
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • (WD repeat-containing protein ...) x 5
  • 18S rRNA18S ribosomal RNA
  • 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


nucleologenesis / preribosome / granular component / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / U4atac snRNP / snoRNA localization / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process ...nucleologenesis / preribosome / granular component / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / U4atac snRNP / snoRNA localization / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / U4atac snRNA binding / nuclear retention of unspliced pre-mRNA at the site of transcription / nuclear polyadenylation-dependent CUT catabolic process / transcription elongation regulator activity / regulation of telomerase RNA localization to Cajal body / positive regulation of male gonad development / nuclear polyadenylation-dependent tRNA catabolic process / CURI complex / regulation of transcription elongation from RNA polymerase II promoter / nuclear polyadenylation-dependent rRNA catabolic process / t-UTP complex / CUT catabolic process / UTP-C complex / exosome (RNase complex) / Pwp2p-containing subcomplex of 90S preribosome / nuclear exosome (RNase complex) / rRNA (adenine-N6,N6-)-dimethyltransferase activity / histone-glutamine methyltransferase activity / polyadenylation-dependent snoRNA 3'-end processing / box C/D RNA binding / box C/D RNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of stem cell population maintenance / Mpp10 complex / pre-snoRNP complex / rRNA methyltransferase activity / nuclear mRNA surveillance / rRNA (pseudouridine) methyltransferase activity / positive regulation of rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / dense fibrillar component / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone methyltransferase binding / histone mRNA catabolic process / blastocyst formation / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / RNA splicing, via transesterification reactions / response to extracellular stimulus / box C/D RNP complex / tRNA export from nucleus / rRNA base methylation / rRNA primary transcript binding / negative regulation of RNA splicing / positive regulation of transcription by RNA polymerase I / ubiquitin ligase inhibitor activity / rRNA modification in the nucleus and cytosol / U2-type precatalytic spliceosome / cytoplasmic side of rough endoplasmic reticulum membrane / activation-induced cell death of T cells / telomerase RNA binding / sno(s)RNA-containing ribonucleoprotein complex / response to stimulus / dosage compensation by inactivation of X chromosome / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process / histone glutamine methylation / U4 snRNA binding / negative regulation of ubiquitin protein ligase activity / SUMOylation of RNA binding proteins / Formation of the ternary complex, and subsequently, the 43S complex / box C/D snoRNP assembly / erythrocyte homeostasis / U3 snoRNA binding / blastocyst development / negative regulation of telomere maintenance via telomerase / Cul4-RING E3 ubiquitin ligase complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / endoplasmic reticulum mannose trimming / translation regulator activity / 90S preribosome / TFIID-class transcription factor complex binding / preribosome, small subunit precursor / precatalytic spliceosome / mRNA Splicing - Minor Pathway / cytoplasmic pattern recognition receptor signaling pathway / modulation by symbiont of host defense response / positive regulation of cellular component movement / Peptide chain elongation / erythrocyte development / endoplasmic reticulum quality control compartment / Association of TriC/CCT with target proteins during biosynthesis / Selenocysteine synthesis / TOR signaling / fibroblast growth factor binding / Formation of a pool of free 40S subunits / RNA polymerase II complex binding
Similarity search - Function
Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1 / Active regulator of SIRT1 / Nucleolar protein 7 / Rrp7A, RNA recognition motif / NUC129 domain / Nucleolar protein 7, C-terminal / Exosome-associated factor Rrp6, N-terminal / PMC2NT (NUC016) domain / Down-regulated in metastasis / Down-regulated-in-metastasis protein ...Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1 / Active regulator of SIRT1 / Nucleolar protein 7 / Rrp7A, RNA recognition motif / NUC129 domain / Nucleolar protein 7, C-terminal / Exosome-associated factor Rrp6, N-terminal / PMC2NT (NUC016) domain / Down-regulated in metastasis / Down-regulated-in-metastasis protein / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / Ribosomal RNA adenine dimethylase / rRNA-processing protein Fcf1, PIN domain / Nrap protein, domain 3 / Sof1-like protein / Nrap protein domain 1 / Small-subunit processome, Utp11 / BING4, C-terminal domain / NOL6/Upt22 / Nrap protein, domain 5 / Fcf2 pre-rRNA processing, C-terminal / Nrap protein, domain 4 / Nrap protein, domain 6 / Nrap protein domain 1 / BING4CT (NUC141) domain / Nrap protein domain 6 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein domain 3 / Nrap protein PAP/OAS-like domain / Fcf2 pre-rRNA processing / BING4CT (NUC141) domain / Sof1-like domain / Utp11 protein / Nrap protein, domain 2 / WD repeat-containing protein WDR46/Utp7 / Fcf2/DNTTIP2 / rRNA-processing protein Fcf1/Utp23 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / U3 small nucleolar RNA-associated protein 6 / Rrp7 RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 / Fcf1 / Ribosomal RNA-processing protein 7, C-terminal domain / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 6 / UTP15 C terminal / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 15, C-terminal / Sas10 C-terminal domain / Sas10 C-terminal domain / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / NOP5NT (NUC127) domain / NOP5, N-terminal / Helicase and RNase D C-terminal / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / RNA 3'-terminal phosphate cyclase signature. / Ribosomal RNA adenine dimethylase / Utp13 specific WD40 associated domain / rRNA adenine N(6)-methyltransferase family profile. / Ribosomal RNA adenine methyltransferase KsgA/Erm / Small-subunit processome, Utp13 / HRDC domain / Periodic tryptophan protein 2 / U3 small nucleolar RNA-associated protein 10, N-terminal / BP28CT (NUC211) domain / Sas10/Utp3/C1D family / U3 small nucleolar RNA-associated protein 10 / HRDC domain profile. / BP28CT (NUC211) domain / BP28, C-terminal domain / Sas10/Utp3/C1D / HRDC domain / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Ribosomal RNA-processing protein Rrp9-like / Dip2/Utp12 Family / Small-subunit processome, Utp12 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Small-subunit processome, Utp21 / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / Pre-rRNA-processing protein PNO1-like / RNA 3'-terminal phosphate cyclase (RTC), insert domain / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase / Fibrillarin / Fibrillarin, conserved site / Fibrillarin signature.
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 15 homolog / WD repeat-containing protein 36 / Probable ATP-dependent RNA helicase DHX37 / WD repeat-containing protein 75 / U3 small nucleolar ribonucleoprotein protein IMP4 / Active regulator of SIRT1 / Deoxynucleotidyltransferase terminal-interacting protein 2 / Periodic tryptophan protein 2 homolog / WD repeat-containing protein 43 ...Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 15 homolog / WD repeat-containing protein 36 / Probable ATP-dependent RNA helicase DHX37 / WD repeat-containing protein 75 / U3 small nucleolar ribonucleoprotein protein IMP4 / Active regulator of SIRT1 / Deoxynucleotidyltransferase terminal-interacting protein 2 / Periodic tryptophan protein 2 homolog / WD repeat-containing protein 43 / Ribosome biogenesis protein BMS1 homolog / Transducin beta-like protein 3 / Exosome component 10 / Ubiquitin-40S ribosomal protein S27a / U3 small nucleolar RNA-associated protein 4 homolog / DDB1- and CUL4-associated factor 13 / U3 small nucleolar RNA-associated protein 14 homolog A / Nucleolar protein 58 / Probable U3 small nucleolar RNA-associated protein 11 / rRNA-processing protein FCF1 homolog / U3 small nucleolar RNA-associated protein 6 homolog / Nucleolar protein 7 / Probable dimethyladenosine transferase / WD repeat-containing protein 3 / Ribosomal RNA-processing protein 7 homolog A / HEAT repeat-containing protein 1 / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein S24 / U3 small nucleolar ribonucleoprotein protein IMP3 / RNA-binding protein PNO1 / Something about silencing protein 10 / Nucleolar protein 6 / 40S ribosomal protein S28 / ADENOSINE-5'-TRIPHOSPHATE / 40S ribosomal protein S6 / 40S ribosomal protein S17 / S-ADENOSYL-L-HOMOCYSTEINE / : / : / : / GUANOSINE-5'-TRIPHOSPHATE / 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 / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S8 / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S23 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S15a / 40S ribosomal protein S7 / 40S ribosomal protein S12 / 40S ribosomal protein S3a / NHP2-like protein 1 / 40S ribosomal protein S5 / 40S ribosomal protein S9 / 40S ribosomal protein S27 / 40S ribosomal protein S19 / 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: [Figure: see text].
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

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Structure visualization

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Structure viewerMolecule:
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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
Water0
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 / 18S ribosomal RNA


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 / Ribosome / 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 / Nucleolus


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 / Nucleolus / 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 / Nucleolus / 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 / Nucleolus / 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 / Nucleolus / 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 / Nucleolus


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)

+
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 / Adenosine 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 / Guanosine 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 / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

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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 FIELDBright-field microscopy / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm
Specimen holderModel: 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-ID
15WLC1
26ZQD1
36ZOJ1
42IPX1
52OZB1
64JXM1
75FAI1
86G181
96G4S1
106O161
116W6C1

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