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- PDB-5wlc: The complete structure of the small subunit processome -

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Basic information

Entry
Database: PDB / ID: 5wlc
TitleThe complete structure of the small subunit processome
Components
  • 18S pre-rRNA
  • 5' ETS
  • Bms1
  • Bud21
  • Emg1
  • Enp1
  • Enp2
  • Faf1
  • Fcf2
  • Imp3
  • Imp4
  • Kre33
  • Krr1
  • Lcp5
  • Mpp10
  • Noc4
  • Nop1
  • Nop14
  • Nop56
  • Nop58
  • Pno1
  • Rcl1
  • Rrp5
  • Rrp7
  • Rrp9
  • Rrt14
  • Sas10
  • Snu13
  • Sof1
  • U3 snoRNA
  • Unassigned peptides
  • Utp1
  • Utp10
  • Utp11
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp17
  • Utp18
  • Utp20
  • Utp21
  • Utp22
  • Utp24
  • Utp30
  • Utp4
  • Utp5
  • Utp6
  • Utp7
  • Utp8
  • Utp9
  • rpS11_uS17
  • rpS13_uS15
  • rpS14_uS11
  • rpS16_uS9
  • rpS18_uS13
  • rpS22_uS8
  • rpS23_uS12
  • rpS24_eS24
  • rpS28_eS28
  • rpS4_eS4
  • rpS5_uS7
  • rpS6_eS6
  • rpS7_eS7
  • rpS8_eS8
  • rpS9_uS4
KeywordsRIBOSOME / Ribosome assembly
Function / homology
Function and homology information


tRNA wobble cytosine modification / regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / tRNA acetylation ...tRNA wobble cytosine modification / regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / tRNA acetylation / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / box C/D sno(s)RNA binding / regulation of rRNA processing / septum digestion after cytokinesis / snRNA binding / tRNA re-export from nucleus / 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) / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / O-methyltransferase activity / small nuclear ribonucleoprotein complex / 90S preribosome assembly / rRNA methylation / histone H2AQ104 methyltransferase activity / mTORC1-mediated signalling / mRNA modification / U4 snRNP / U3 snoRNA binding / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / snoRNA binding / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / nucleolar large rRNA transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / proteasome assembly / ribosomal subunit export from nucleus / RNA processing / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U4/U6 x U5 tri-snRNP complex / ribosomal small subunit export from nucleus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / nuclear periphery / enzyme activator activity / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / spliceosomal complex / mRNA splicing, via spliceosome / maintenance of translational fidelity / rRNA processing / unfolded protein binding / peroxisome / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly
Similarity search - Function
Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / : / NUC153 / Nucleolar protein 10/Enp2 / : / : / NUC153 domain / Nucleolar protein 10-like, second domain / Nucleolar protein 10-like, N-terminal domain ...Regulator of rDNA transcription 14 / Regular of rDNA transcription protein 14 / : / NUC153 / Nucleolar protein 10/Enp2 / : / : / NUC153 domain / Nucleolar protein 10-like, second domain / Nucleolar protein 10-like, N-terminal domain / U3 small nucleolar RNA-associated protein 8 / : / Utp8, N-terminal beta propeller / Utp8, C-terminal / rRNA biogenesis protein Rrp5 / : / : / U3 snoRNA associated / Nucleolar complex protein 4 / U3 snoRNA associated / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10/TcmA, helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Nucleolar protein 14 / Nop14-like family / 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 / : / 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
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rps5p / KRR1 small subunit processome component / Regulator of rDNA transcription 14 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rps5p / KRR1 small subunit processome component / Regulator of rDNA transcription 14 / U3 small nucleolar RNA-associated protein 11 / Regulator of rDNA transcription 14 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Small ribosomal subunit protein uS12A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / Periodic tryptophan protein 2 / Small ribosomal subunit protein eS7A / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar ribonucleoprotein protein LCP5 / U3 small nucleolar RNA-associated protein 18 / Protein FAF1 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / Ribosome biogenesis protein ENP2 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar RNA-associated protein 8 / RNA cytidine acetyltransferase / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 14 / rRNA biogenesis protein RRP5 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / rRNA processing protein RCL1 / U3 small nucleolar RNA-associated protein 16 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / Small ribosomal subunit protein eS28A / Nucleolar complex protein 14 / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBarandun, J. / Chaker-Margot, M. / Hunziker, M. / Klinge, S.
Funding support United States, European Union, Switzerland, Canada, France, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
European Molecular Biology Organization (EMBO)ALTF 51-2014European Union
Swiss National Science Foundation155515 Switzerland
Natural Sciences and Engineering Research Council (NSERC, Canada)PGS-D Canada
Human Frontier Science Program (HFSP) France
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: The complete structure of the small-subunit processome.
Authors: Jonas Barandun / Malik Chaker-Margot / Mirjam Hunziker / Kelly R Molloy / Brian T Chait / Sebastian Klinge /
Abstract: The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit ...The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.
History
DepositionJul 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
L0: 5' ETS
L1: 18S pre-rRNA
L2: U3 snoRNA
L3: rpS18_uS13
L4: rpS4_eS4
L5: rpS5_uS7
L6: rpS6_eS6
L7: rpS7_eS7
L8: rpS8_eS8
L9: rpS9_uS4
LC: rpS16_uS9
LD: rpS11_uS17
LE: rpS22_uS8
LF: rpS24_eS24
LG: rpS28_eS28
LH: Utp17
LI: Utp8
LJ: Utp15
LK: Utp9
LL: Utp5
LM: Utp10
LN: Utp4
LO: Utp1
LP: Utp6
LQ: Utp12
LR: Utp13
LS: Utp18
LT: Utp21
LU: Sof1
LV: Enp2
LW: Utp7
LX: Kre33
LY: Kre33
LZ: Imp3
NA: Mpp10
NB: Sas10
NC: Lcp5
ND: Bud21
NE: Faf1
NF: rpS13_uS15
NG: rpS14_uS11
NH: Utp22
NI: Rrp7
NJ: Rrp5
NK: Krr1
SA: Nop56
SB: Nop58
SC: Nop1
SD: Nop1
SE: Snu13
SF: Snu13
SG: Rrp9
SH: Rcl1
SI: Bms1
SJ: Emg1
SK: Emg1
SL: Utp24
SM: Imp4
SN: Utp30
SO: Pno1
SP: Utp20
SQ: Fcf2
SR: rpS23_uS12
SS: Utp14
ST: Nop14
SU: Noc4
SV: Rrt14
SX: Unassigned peptides
SY: Utp11
SZ: Enp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,499,17571
Polymers4,499,11070
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
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


Mass: 225543.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 1262303
#2: RNA chain 18S pre-rRNA


Mass: 582052.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 874346701
#3: RNA chain U3 snoRNA


Mass: 106503.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: GenBank: 176452

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Protein , 63 types, 67 molecules L3L4L5L6L7L8L9LCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLXLY...

#4: Protein rpS18_uS13


Mass: 16773.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX55
#5: Protein rpS4_eS4


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX35
#6: Protein rpS5_uS7


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: A0A1L4AA68
#7: Protein rpS6_eS6


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX37
#8: Protein rpS7_eS7


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P26786
#9: Protein rpS8_eS8


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX39
#10: Protein rpS9_uS4


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: O13516
#11: Protein rpS16_uS9


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX51
#12: Protein rpS11_uS17


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX47
#13: Protein rpS22_uS8


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0C0W1
#14: Protein rpS24_eS24


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CX31
#15: Protein rpS28_eS28


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q3E7X9
#16: Protein Utp17


Mass: 100960.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q02931
#17: Protein Utp8


Mass: 65572.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53276
#18: Protein Utp15


Mass: 57765.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04305
#19: Protein Utp9


Mass: 64378.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P38882
#20: Protein Utp5


Mass: 72079.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04177
#21: Protein Utp10


Mass: 200020.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P42945
#22: Protein Utp4


Mass: 87316.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06679
#23: Protein Utp1


Mass: 104097.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P25635
#24: Protein Utp6


Mass: 48437.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q02354
#25: Protein Utp12


Mass: 105037.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12220
#26: Protein Utp13


Mass: 75035.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q05946
#27: Protein Utp18


Mass: 66494.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40362
#28: Protein Utp21


Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06078
#29: Protein Sof1


Mass: 56888.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P33750
#30: Protein Enp2


Mass: 81864.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P48234
#31: Protein Utp7


Mass: 62418.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40055
#32: Protein Kre33


Mass: 95337.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
References: UniProt: P53914, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#33: Protein Imp3


Mass: 21928.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P32899
#34: Protein Mpp10


Mass: 67042.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P47083
#35: Protein Sas10


Mass: 69705.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12136
#36: Protein Lcp5


Mass: 40864.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40079
#37: Protein Bud21


Mass: 23835.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08492
#38: Protein Faf1


Mass: 38173.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P40546
#39: Protein rpS13_uS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P05756
#40: Protein rpS14_uS11


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P06367
#41: Protein Utp22


Mass: 140660.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53254
#42: Protein Rrp7


Mass: 34526.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P25368
#43: Protein Rrp5


Mass: 193411.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q05022
#44: Protein Krr1


Mass: 37226.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: B3LU25
#45: Protein Nop56


Mass: 56394.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12460
#46: Protein Nop58


Mass: 53814.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12499
#47: Protein Nop1


Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#48: Protein Snu13


Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P39990
#49: Protein Rrp9


Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06506
#50: Protein Rcl1


Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08096
#51: Protein Bms1


Mass: 135152.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q08965
#52: Protein Emg1


Mass: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
References: UniProt: Q06287, rRNA small subunit pseudouridine methyltransferase Nep1
#53: Protein Utp24


Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q05498
#54: Protein Imp4


Mass: 33536.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P53941
#55: Protein Utp30


Mass: 31668.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P36144
#56: Protein Pno1


Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q99216
#57: Protein Utp20


Mass: 83590.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
#58: Protein Fcf2


Mass: 25689.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q12035
#59: Protein rpS23_uS12


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P0CY39
#60: Protein Utp14


Mass: 101101.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q04500
#61: Protein Nop14


Mass: 85993.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q99207
#62: Protein Noc4


Mass: 58369.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: Q06512
#63: Protein Rrt14


Mass: 21036.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: B5VKI1, UniProt: E9P9B2
#64: Protein Unassigned peptides


Mass: 8783.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
#65: Protein Utp11


Mass: 29806.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: B5VM59
#66: Protein Enp1


Mass: 55207.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741 / References: UniProt: P38333

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Non-polymers , 1 types, 1 molecules

#67: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Small subunit processome / Type: COMPLEX / Entity ID: #1-#66 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(HOCH2)3CNH21
2150 mMsodium chlorideNaCl1
31 mMEDTA(HO2CCH2)2NCH2CH2N(CH2CO2H)21
40.1 %Triton X-1001
55 mMbiotin1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ted Pella Inc.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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 magnification: 22500 X / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 10029
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.12rc1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 772120
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284213 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 338.9 / Protocol: OTHER / Space: REAL

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