- PDB-5wlc: The complete structure of the small subunit processome -
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Basic information
Entry
Database: PDB / ID: 5wlc
Title
The 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)
Snu13NHP2L1
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
Keywords
RIBOSOME / Ribosome assembly
Function / homology
Function and homology information
rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / 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) / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome ...rRNA acetylation involved in maturation of SSU-rRNA / Noc4p-Nop14p complex / rRNA cytidine N-acetyltransferase activity / CURI complex / t-UTP complex / 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) / sno(s)RNA processing / Pwp2p-containing subcomplex of 90S preribosome / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / mRNA modification / histone-glutamine methyltransferase activity / box C/D RNA binding / box C/D RNA 3'-end processing / Mpp10 complex / box H/ACA snoRNA binding / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA 2'-O-methylation / septum digestion after cytokinesis / rRNA modification / regulation of transcription by RNA polymerase I / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / rDNA heterochromatin / 90S preribosome assembly / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP 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 / U4 snRNA binding / histone glutamine methylation / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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) / enzyme activator activity / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / cytosolic small ribosomal subunit / unfolded protein binding / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / cell cycle / ATPase activity / 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 S23-A / Periodic tryptophan protein 2 / 40S ribosomal protein S7-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / U3 small nucleolar RNA-associated protein 13 / 40S ribosomal protein S11-A / Protein SOF1 / 40S ribosomal protein S8-A ...40S ribosomal protein S18-A / 40S ribosomal protein S23-A / Periodic tryptophan protein 2 / 40S ribosomal protein S7-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / U3 small nucleolar RNA-associated protein 13 / 40S ribosomal protein S11-A / Protein SOF1 / 40S ribosomal protein S8-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S24-A / 40S ribosomal protein S22-A / 40S ribosomal protein S14-A / 40S ribosomal protein S13 / 40S ribosomal protein S9-A / Regulator of rDNA transcription 14 / U3 small nucleolar RNA-associated protein 11 / Regulator of rDNA transcription 14 / KRR1 small subunit processome component / 40S ribosomal protein S5 / U3 small nucleolar ribonucleoprotein protein IMP3 / U3 small nucleolar RNA-associated protein 9 / Ribosome biogenesis protein UTP30 / U3 small nucleolar RNA-associated protein 12 / gb:874346701: / gb:1262303: / Pre-rRNA-processing protein PNO1 / Nucleolar complex protein 14 / 40S ribosomal protein S28-A / Nucleolar protein 58 / Nucleolar protein 56 / Something about silencing protein 10 / rRNA-processing protein FCF1 / rRNA-processing protein FCF2 / Ribosome biogenesis protein BMS1 / Bud site selection protein 21 / 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 / gb:176452: / rRNA biogenesis protein RRP5 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 21 / 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 / Ribosome biogenesis protein ENP2 / U3 small nucleolar RNA-associated protein 14 / 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 / Ribosomal RNA-processing protein 7
Biological species
Saccharomyces cerevisiae BY4741 (yeast)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
United States, European Union, Switzerland, Canada, France, 5items
Organization
Grant number
Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
1DP2GM123459
United States
European Molecular Biology Organization (EMBO)
ALTF 51-2014
European Union
Swiss National Science Foundation
155515
Switzerland
Natural Sciences and Engineering Research Council (NSERC, Canada)
PGS-D
Canada
Human Frontier Science Program (HFSP)
France
Citation
Journal: 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.
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
18Spre-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
U3snoRNA
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 / NHP2L1
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
Unassignedpeptides
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
Average 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 scans
Movie frames/image: 32
-
Processing
EM software
ID
Name
Version
Category
1
RELION
2
particleselection
2
SerialEM
imageacquisition
4
CTFFIND
4
CTFcorrection
7
Coot
0.8.9
modelfitting
9
RELION
2
initialEulerassignment
10
RELION
2
finalEulerassignment
11
RELION
2
classification
12
RELION
2
3Dreconstruction
13
PHENIX
1.12rc1
modelrefinement
CTF correction
Type: NONE
Particle selection
Num. of particles selected: 772120
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284213 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model building
B value: 338.9 / Protocol: OTHER / Space: REAL
+
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