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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
  • Sas10SAS (TV station)
  • 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


rRNA acetylation involved in maturation of SSU-rRNA / box H/ACA snoRNA binding / Noc4p-Nop14p complex / CURI complex / t-UTP complex / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snoRNA processing ...rRNA acetylation involved in maturation of SSU-rRNA / box H/ACA snoRNA binding / Noc4p-Nop14p complex / CURI complex / t-UTP complex / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snoRNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / box C/D snoRNA 3'-end processing / mRNA modification / box C/D snoRNA binding / Mpp10 complex / rRNA methyltransferase activity / regulation of transcription by RNA polymerase I / septum digestion after cytokinesis / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / positive regulation of RNA binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome assembly / box C/D snoRNP complex / rRNA primary transcript binding / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / small nuclear ribonucleoprotein complex / protein localization to nucleolus / U3 snoRNA binding / U4 snRNA binding / histone glutamine methylation / Cul4-RING E3 ubiquitin ligase complex / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / small nucleolar ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / preribosome, small subunit precursor / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 90S preribosome / O-methyltransferase activity / rRNA methylation / snoRNA binding / poly(U) RNA binding / 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) / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / small-subunit processome / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / ribosomal small subunit biogenesis / nuclear periphery / proteasome assembly / maturation of LSU-rRNA / Cajal body / endoribonuclease activity / establishment of cell polarity / positive regulation of translational fidelity / enzyme activator activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / ribosome biogenesis / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / cell cycle / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Bystin / Ribosomal protein L1/ribosomal biogenesis protein / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic ...Bystin / Ribosomal protein L1/ribosomal biogenesis protein / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Regulator of rDNA transcription 14 / Possible tRNA binding domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleolar complex protein 4 / Periodic tryptophan protein 2 / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA-processing protein 7, C-terminal domain / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S7 domain / Ribosomal protein S8 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / WD40-repeat-containing domain superfamily / Nop domain superfamily / Nrap protein, domain 6 / 40S ribosomal protein S11, N-terminal / Nrap protein, domain 5 / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / Nrap protein domain 1 / RNA cytidine acetyltransferase NAT10 / TmcA/NAT10/Kre33 / Ribosomal RNA assembly KRR1 / RNA 3'-terminal phosphate cyclase domain / Ribosome biogenesis protein Bms1, N-terminal / Fcf2 pre-rRNA processing, C-terminal / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / RNA 3'-terminal phosphate cyclase type 2 / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein S13, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / U3 small nucleolar RNA-associated protein 6 / Small-subunit processome, Utp13 / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L1-like / Ribosomal protein S7, conserved site / Ribosomal protein S15P / RNA-binding domain, S1 / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / U3 small nucleolar RNA-associated protein 10, N-terminal / HEAT, type 2 / Fibrillarin, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / WD40 repeat, conserved site / U3 small nucleolar RNA-associated protein 15, C-terminal / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 8 / Ribosomal protein L7Ae/L8/Nhp2 family / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosomal protein S4e, central domain superfamily / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / Nrap protein domain 3 / Krr1 KH1 domain / S1 RNA binding domain / Rrp7 RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Nrap protein domain 6 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS-like domain / NOP5NT (NUC127) domain / Nrap protein domain 1 / Ribosomal protein S11 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S15 / U3 snoRNA associated / Sas10 C-terminal domain / Sas10/Utp3/C1D family / snoRNA binding domain, fibrillarin
40S ribosomal protein S18-A / 40S ribosomal protein S13 / U3 small nucleolar RNA-associated protein 11 / Regulator of rDNA transcription 14 / KRR1 small subunit processome component / RPS5 isoform 1 / 40S ribosomal protein S23-A / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S16-A / 40S ribosomal protein S6-A ...40S ribosomal protein S18-A / 40S ribosomal protein S13 / U3 small nucleolar RNA-associated protein 11 / Regulator of rDNA transcription 14 / KRR1 small subunit processome component / RPS5 isoform 1 / 40S ribosomal protein S23-A / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S16-A / 40S ribosomal protein S6-A / 40S ribosomal protein S11-A / 40S ribosomal protein S8-A / 40S ribosomal protein S14-A / 40S ribosomal protein S4-A / 40S ribosomal protein S7-A / Regulator of rDNA transcription 14 / 40S ribosomal protein S9-A / 40S ribosomal protein S24-A / 40S ribosomal protein S22-A / Periodic tryptophan protein 2 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar ribonucleoprotein protein IMP3 / Ribosome biogenesis protein BMS1 / Pre-rRNA-processing protein PNO1 / Nucleolar complex protein 14 / 40S ribosomal protein S28-A / Nucleolar protein 58 / Nucleolar protein 56 / U3 small nucleolar RNA-associated protein 12 / Something about silencing protein 10 / rRNA-processing protein FCF2 / Bud site selection protein 21 / gb:874346701: / RNA 3'-terminal phosphate cyclase-like protein / U3 small nucleolar RNA-associated protein 4 / Nucleolar complex protein 4 / Ribosomal RNA-processing protein 9 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / gb:1262303: / gb:176452: / rRNA biogenesis protein RRP5 / Protein FAF1 / 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 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 15 / 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 / Ribosomal RNA-processing protein 7
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.
Validation Report
SummaryFull reportAbout validation report
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

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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
Water0
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 / SAS (TV station)


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

-
Non-polymers , 1 types, 1 molecules

#67: Chemical ChemComp-ZN / ZINC ION / Zinc


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

-
Experimental details

-
Experiment

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

-
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 chlorideNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acid(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

-
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 magnification: 22500 X / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / 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

-
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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