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- EMDB-32795: Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Ts... -

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Basic information

Entry
Database: EMDB / ID: EMD-32795
TitleCryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (without Rps2)
Map data
Sample
  • Complex: Yeast pre-40S ribosomal subunit
    • RNA: x 1 types
    • Protein or peptide: x 17 types
  • Ligand: x 1 types
Function / homology
Function and homology information


18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mTORC1-mediated signalling / Protein hydroxylation / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex ...18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mTORC1-mediated signalling / Protein hydroxylation / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 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) / regulation of translational fidelity / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / unfolded protein binding / ribosome biogenesis / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Methyltransferase type 11 / Methyltransferase domain / Krr1, KH1 domain / Krr1 KH1 domain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain ...18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / Methyltransferase type 11 / Methyltransferase domain / Krr1, KH1 domain / Krr1 KH1 domain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / K Homology domain, type 1 superfamily / : / Ribosomal protein S30 / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / : / Ribosomal protein S17, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal S11, conserved site / Ribosomal protein S8 / Ribosomal protein S17 signature. / S4 RNA-binding domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S8 signature. / Ribosomal protein S11 / S4 domain / Ribosomal protein S17/S11 / Ribosomal protein S4 signature. / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S12/S23 / S4 RNA-binding domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal protein S11 signature. / Ribosomal protein S11 superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A ...Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / 18S rRNA (guanine(1575)-N(7))-methyltransferase / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Ribosome biogenesis protein TSR1 / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsCheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2022
Title: The nucleoplasmic phase of pre-40S formation prior to nuclear export.
Authors: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
History
DepositionFeb 5, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32795.png

Downloads & links

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Map

FileDownload / File: emd_32795.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.13289551 - 0.2902426
Average (Standard dev.)0.00020894622 (±0.0065830057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast pre-40S ribosomal subunit

EntireName: Yeast pre-40S ribosomal subunit
Components
  • Complex: Yeast pre-40S ribosomal subunit
    • RNA: 18S rRNA18S ribosomal RNA
    • Protein or peptide: 40S ribosomal protein S1-ARibosome
    • Protein or peptide: 40S ribosomal protein S4-ARibosome
    • Protein or peptide: 40S ribosomal protein S6-ARibosome
    • Protein or peptide: 40S ribosomal protein S7-ARibosome
    • Protein or peptide: 40S ribosomal protein S8-ARibosome
    • Protein or peptide: 40S ribosomal protein S9-ARibosome
    • Protein or peptide: 40S ribosomal protein S11-ARibosome
    • Protein or peptide: 40S ribosomal protein S13
    • Protein or peptide: 40S ribosomal protein S14-ARibosome
    • Protein or peptide: 40S ribosomal protein S22-ARibosome
    • Protein or peptide: 40S ribosomal protein S23-ARibosome
    • Protein or peptide: 40S ribosomal protein S24-ARibosome
    • Protein or peptide: 40S ribosomal protein S27-ARibosome
    • Protein or peptide: 40S ribosomal protein S30-ARibosome
    • Protein or peptide: Pre-rRNA-processing protein PNO1
    • Protein or peptide: 18S rRNA (guanine(1575)-N(7))-methyltransferase
    • Protein or peptide: Ribosome biogenesis protein TSR1
  • Ligand: ZINC ION

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Supramolecule #1: Yeast pre-40S ribosomal subunit

SupramoleculeName: Yeast pre-40S ribosomal subunit / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: 18S rRNA

MacromoleculeName: 18S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 579.761938 KDa
SequenceString: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGUAUAAC UGUGGUAAUU C UAGAGCUA ...String:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGUAUAAC UGUGGUAAUU C UAGAGCUA AUACAUGCUU AAAAUCUCGA CCCUUUGGAA GAGAUGUAUU UAUUAGAUAA AAAAUCAAUG UCUUCGGACU CU UUGAUGA UUCAUAAUAA CUUUUCGAAU CGCAUGGCCU UGUGCUGGCG AUGGUUCAUU CAAAUUUCUG CCCUAUCAAC UUU CGAUGG UAGGAUAGUG GCCUACCAUG GUUUCAACGG GUAACGGGGA AUAAGGGUUC GAUUCCGGAG AGGGAGCCUG AGAA ACGGC UACCACAUCC AAGGAAGGCA GCAGGCGCGC AAAUUACCCA AUCCUAAUUC AGGGAGGUAG UGACAAUAAA UAACG AUAC AGGGCCCAUU CGGGUCUUGU AAUUGGAAUG AGUACAAUGU AAAUACCUUA ACGAGGAACA AUUGGAGGGC AAGUCU GGU GCCAGCAGCC GCGGUAAUUC CAGCUCCAAU AGCGUAUAUU AAAGUUGUUG CAGUUAAAAA GCUCGUAGUU GAACUUU GG GCCCGGUUGG CCGGUCCGAU UUUUUCGUGU ACUGGAUUUC CAACGGGGCC UUUCCUUCUG GCUAACCUUG AGUCCUUG U GGCUCUUGGC GAACCAGGAC UUUUACUUUG AAAAAAUUAG AGUGUUCAAA GCAGGCGUAU UGCUCGAAUA UAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUU CAAUUGUCAG AGGUGAAAUU CUUGGAUUUA UUGAAGACUA ACUACUGCGA AAGCAUUUGC CAAGGACGUU U UCAUUAAU CAAGAACGAA AGUUAGGGGA UCGAAGAUGA UCAGAUACCG UCGUAGUCUU AACCAUAAAC UAUGCCGACU AG GGAUCGG GUGGUGUUUU UUUAAUGACC CACUCGGCAC CUUACGAGAA AUCAAAGUCU UUGGGUUCUG GGGGGAGUAU GGU CGCAAG GCUGAAACUU AAAGGAAUUG ACGGAAGGGC ACCACCAGGA GUGGAGCCUG CGGCUUAAUU UGACUCAACA CGGG GAAAC UCACCAGGUC CAGACACAAU AAGGAUUGAC AGAUUGAGAG CUCUUUCUUG AUUUUGUGGG UGGUGGUGCA UGGCC GUUC UUAGUUGGUG GAGUGAUUUG UCUGCUUAAU UGCGAUAACG AACGAGACCU UAACCUACUA AAUAGUGGUG CUAGCA UUU GCUGGUUAUC CACUUCUUAG AGGGACUAUC GGUUUCAAGC CGAUGGAAGU UUGAGGCAAU AACAGGUCUG UGAUGCC CU UAGACGUUCU GGGCCGCACG CGCGCUACAC UGACGGAGCC AGCGAGUCUA ACCUUGGCCG AGAGGUCUUG GUAAUCUU G UGAAACUCCG UCGUGCUGGG GAUAGAGCAU UGUAAUUAUU GCUCUUCAAC GAGGAAUUCC UAGUAAGCGC AAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUA GAGAAGGGGG CAACUCCAUC UCAGAGCGGA GAAUUUGGAC AAACUUGGUC AUUUAGAGGA ACUAAAAGUC G UAACAAGG UUUCCGUAGG UGAACCUGCG GAAGGAUCAU UA

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Macromolecule #2: 40S ribosomal protein S1-A

MacromoleculeName: 40S ribosomal protein S1-A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 28.798467 KDa
SequenceString: MAVGKNKRLS KGKKGQKKRV VDPFTRKEWF DIKAPSTFEN RNVGKTLVNK STGLKSASDA LKGRVVEVCL ADLQGSEDHS FRKIKLRVD EVQGKNLLTN FHGMDFTTDK LRSMVRKWQT LIEANVTVKT SDDYVLRIFA IAFTRKQANQ VKRHSYAQSS H IRAIRKVI ...String:
MAVGKNKRLS KGKKGQKKRV VDPFTRKEWF DIKAPSTFEN RNVGKTLVNK STGLKSASDA LKGRVVEVCL ADLQGSEDHS FRKIKLRVD EVQGKNLLTN FHGMDFTTDK LRSMVRKWQT LIEANVTVKT SDDYVLRIFA IAFTRKQANQ VKRHSYAQSS H IRAIRKVI SEILTKEVQG STLAQLTSKL IPEVINKEIE NATKDIFPLQ NIHVRKVKLL KQPKFDVGAL MALHGEGSGE EK GKKVTGF KDEVLETV

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Macromolecule #3: 40S ribosomal protein S4-A

MacromoleculeName: 40S ribosomal protein S4-A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 29.46933 KDa
SequenceString: MARGPKKHLK RLAAPHHWLL DKLSGCYAPR PSAGPHKLRE SLPLIVFLRN RLKYALNGRE VKAILMQRHV KVDGKVRTDT TYPAGFMDV ITLDATNENF RLVYDVKGRF AVHRITDEEA SYKLGKVKKV QLGKKGVPYV VTHDGRTIRY PDPNIKVNDT V KIDLASGK ...String:
MARGPKKHLK RLAAPHHWLL DKLSGCYAPR PSAGPHKLRE SLPLIVFLRN RLKYALNGRE VKAILMQRHV KVDGKVRTDT TYPAGFMDV ITLDATNENF RLVYDVKGRF AVHRITDEEA SYKLGKVKKV QLGKKGVPYV VTHDGRTIRY PDPNIKVNDT V KIDLASGK ITDFIKFDAG KLVYVTGGRN LGRIGTIVHK ERHDGGFDLV HIKDSLDNTF VTRLNNVFVI GEQGKPYISL PK GKGIKLS IAEERDRRRA QQGL

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Macromolecule #4: 40S ribosomal protein S6-A

MacromoleculeName: 40S ribosomal protein S6-A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.054486 KDa
SequenceString: MKLNISYPVN GSQKTFEIDD EHRIRVFFDK RIGQEVDGEA VGDEFKGYVF KISGGNDKQG FPMKQGVLLP TRIKLLLTKN VSCYRPRRD GERKRKSVRG AIVGPDLAVL ALVIVKKGEQ ELEGLTDTTV PKRLGPKRAN NIRKFFGLSK EDDVRDFVIR R EVTKGEKT ...String:
MKLNISYPVN GSQKTFEIDD EHRIRVFFDK RIGQEVDGEA VGDEFKGYVF KISGGNDKQG FPMKQGVLLP TRIKLLLTKN VSCYRPRRD GERKRKSVRG AIVGPDLAVL ALVIVKKGEQ ELEGLTDTTV PKRLGPKRAN NIRKFFGLSK EDDVRDFVIR R EVTKGEKT YTKAPKIQRL VTPQRLQRKR HQRALKVRNA QAQREAAAEY AQLLAKRLSE RKAEKAEIRK RRASSLKA

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Macromolecule #5: 40S ribosomal protein S7-A

MacromoleculeName: 40S ribosomal protein S7-A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 21.658209 KDa
SequenceString:
MSAPQAKILS QAPTELELQV AQAFVELENS SPELKAELRP LQFKSIREID VAGGKKALAI FVPVPSLAGF HKVQTKLTRE LEKKFQDRH VIFLAERRIL PKPSRTSRQV QKRPRSRTLT AVHDKILEDL VFPTEIVGKR VRYLVGGNKI QKVLLDSKDV Q QIDYKLES FQAVYNKLTG KQIVFEIPSE TH

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Macromolecule #6: 40S ribosomal protein S8-A

MacromoleculeName: 40S ribosomal protein S8-A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.537803 KDa
SequenceString: MGISRDSRHK RSATGAKRAQ FRKKRKFELG RQPANTKIGA KRIHSVRTRG GNKKYRALRI ETGNFSWASE GISKKTRIAG VVYHPSNNE LVRTNTLTKA AIVQIDATPF RQWFEAHYGQ TLGKKKNVKE EETVAKSKNA ERKWAARAAS AKIESSVESQ F SAGRLYAC ...String:
MGISRDSRHK RSATGAKRAQ FRKKRKFELG RQPANTKIGA KRIHSVRTRG GNKKYRALRI ETGNFSWASE GISKKTRIAG VVYHPSNNE LVRTNTLTKA AIVQIDATPF RQWFEAHYGQ TLGKKKNVKE EETVAKSKNA ERKWAARAAS AKIESSVESQ F SAGRLYAC ISSRPGQSGR CDGYILEGEE LAFYLRRLTA KK

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Macromolecule #7: 40S ribosomal protein S9-A

MacromoleculeName: 40S ribosomal protein S9-A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.487893 KDa
SequenceString: MPRAPRTYSK TYSTPKRPYE SSRLDAELKL AGEFGLKNKK EIYRISFQLS KIRRAARDLL TRDEKDPKRL FEGNALIRRL VRVGVLSED KKKLDYVLAL KVEDFLERRL QTQVYKLGLA KSVHHARVLI TQRHIAVGKQ IVNIPSFMVR LDSEKHIDFA P TSPFGGAR ...String:
MPRAPRTYSK TYSTPKRPYE SSRLDAELKL AGEFGLKNKK EIYRISFQLS KIRRAARDLL TRDEKDPKRL FEGNALIRRL VRVGVLSED KKKLDYVLAL KVEDFLERRL QTQVYKLGLA KSVHHARVLI TQRHIAVGKQ IVNIPSFMVR LDSEKHIDFA P TSPFGGAR PGRVARRNAA RKAEASGEAA DEADEADEE

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Macromolecule #8: 40S ribosomal protein S11-A

MacromoleculeName: 40S ribosomal protein S11-A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.785934 KDa
SequenceString:
MSTELTVQSE RAFQKQPHIF NNPKVKTSKR TKRWYKNAGL GFKTPKTAIE GSYIDKKCPF TGLVSIRGKI LTGTVVSTKM HRTIVIRRA YLHYIPKYNR YEKRHKNVPV HVSPAFRVQV GDIVTVGQCR PISKTVRFNV VKVSAAAGKA NKQFAKF

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Macromolecule #9: 40S ribosomal protein S13

MacromoleculeName: 40S ribosomal protein S13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.059945 KDa
SequenceString:
MGRMHSAGKG ISSSAIPYSR NAPAWFKLSS ESVIEQIVKY ARKGLTPSQI GVLLRDAHGV TQARVITGNK IMRILKSNGL APEIPEDLY YLIKKAVSVR KHLERNRKDK DAKFRLILIE SRIHRLARYY RTVAVLPPNW KYESATASAL VN

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Macromolecule #10: 40S ribosomal protein S14-A

MacromoleculeName: 40S ribosomal protein S14-A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.562655 KDa
SequenceString:
MSNVVQARDN SQVFGVARIY ASFNDTFVHV TDLSGKETIA RVTGGMKVKA DRDESSPYAA MLAAQDVAAK CKEVGITAVH VKIRATGGT RTKTPGPGGQ AALRALARSG LRIGRIEDVT PVPSDSTRKK GGRRGRRL

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Macromolecule #11: 40S ribosomal protein S22-A

MacromoleculeName: 40S ribosomal protein S22-A / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.650062 KDa
SequenceString:
MTRSSVLADA LNAINNAEKT GKRQVLIRPS SKVIIKFLQV MQKHGYIGEF EYIDDHRSGK IVVQLNGRLN KCGVISPRFN VKIGDIEKW TANLLPARQF GYVILTTSAG IMDHEEARRK HVSGKILGFV Y

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Macromolecule #12: 40S ribosomal protein S23-A

MacromoleculeName: 40S ribosomal protein S23-A / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.073896 KDa
SequenceString:
MGKGKPRGLN SARKLRVHRR NNRWAENNYK KRLLGTAFKS SPFGGSSHAK GIVLEKLGIE SKQPNSAIRK CVRVQLIKNG KKVTAFVPN DGCLNFVDEN DEVLLAGFGR KGKAKGDIPG VRFKVVKVSG VSLLALWKEK KEKPRS

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Macromolecule #13: 40S ribosomal protein S24-A

MacromoleculeName: 40S ribosomal protein S24-A / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.362848 KDa
SequenceString:
MSDAVTIRTR KVISNPLLAR KQFVVDVLHP NRANVSKDEL REKLAEVYKA EKDAVSVFGF RTQFGGGKSV GFGLVYNSVA EAKKFEPTY RLVRYGLAEK VEKASRQQRK QKKNRDKKIF GTGKRLAKKV ARRNAD

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Macromolecule #14: 40S ribosomal protein S27-A

MacromoleculeName: 40S ribosomal protein S27-A / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.893391 KDa
SequenceString:
MVLVQDLLHP TAASEARKHK LKTLVQGPRS YFLDVKCPGC LNITTVFSHA QTAVTCESCS TILCTPTGGK AKLSEGTSFR RK

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Macromolecule #15: 40S ribosomal protein S30-A

MacromoleculeName: 40S ribosomal protein S30-A / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.137541 KDa
SequenceString:
MAKVHGSLAR AGKVKSQTPK VEKTEKPKKP KGRAYKRLLY TRRFVNVTLV NGKRRMNPGP SVQ

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Macromolecule #16: Pre-rRNA-processing protein PNO1

MacromoleculeName: Pre-rRNA-processing protein PNO1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.380623 KDa
SequenceString: MVAPTALKKA TVTPVSGQDG GSSRIIGINN TESIDEDDDD DVLLDDSDNN TAKEEVEGEE GSRKTHESKT VVVDDQGKPR FTSASKTQG NKIKFESRKI MVPPHRMTPL RNSWTKIYPP LVEHLKLQVR MNLKTKSVEL RTNPKFTTDP GALQKGADFI K AFTLGFDL ...String:
MVAPTALKKA TVTPVSGQDG GSSRIIGINN TESIDEDDDD DVLLDDSDNN TAKEEVEGEE GSRKTHESKT VVVDDQGKPR FTSASKTQG NKIKFESRKI MVPPHRMTPL RNSWTKIYPP LVEHLKLQVR MNLKTKSVEL RTNPKFTTDP GALQKGADFI K AFTLGFDL DDSIALLRLD DLYIETFEVK DVKTLTGDHL SRAIGRIAGK DGKTKFAIEN ATRTRIVLAD SKIHILGGFT HI RMARESV VSLILGSPPG KVYGNLRTVA SRLKERY

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Macromolecule #17: 18S rRNA (guanine(1575)-N(7))-methyltransferase

MacromoleculeName: 18S rRNA (guanine(1575)-N(7))-methyltransferase / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO / EC number: 18S rRNA (guanine1575-N7)-methyltransferase
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.788227 KDa
SequenceString: MSRPEELAPP EIFYNDSEAH KYTGSTRVQH IQAKMTLRAL ELLNLQPCSF ILDIGCGSGL SGEILTQEGD HVWCGLDISP SMLATGLSR ELEGDLMLQD MGTGIPFRAG SFDAAISISA IQWLCNADTS YNDPKQRLMR FFNTLYAALK KGGKFVAQFY P KNDDQVDD ...String:
MSRPEELAPP EIFYNDSEAH KYTGSTRVQH IQAKMTLRAL ELLNLQPCSF ILDIGCGSGL SGEILTQEGD HVWCGLDISP SMLATGLSR ELEGDLMLQD MGTGIPFRAG SFDAAISISA IQWLCNADTS YNDPKQRLMR FFNTLYAALK KGGKFVAQFY P KNDDQVDD ILQSAKVAGF SGGLVVDDPE SKKNKKYYLV LSSGAPPQGE EQVNLDGVTM DEENVNLKKQ LRQRLKGGKD KE SAKSFIL RKKELMKRRG RKVAKDSKFT GRKRRHRF

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Macromolecule #18: Ribosome biogenesis protein TSR1

MacromoleculeName: Ribosome biogenesis protein TSR1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 90.876539 KDa
SequenceString: MAGHSHRSSL KNGHKSYKSK HASKGALKRL YKGKVEKEPV GTGKPDKQVS KLQRKNKAKQ LRAQRILDSI ENRKLFEGKN GAAKIITIV PLVNDLDPLD ILYKLLKCAD DEGIMVQEVD SKRIFNVHIK KFKSNLKIII PDMTNFLNIL DCAKVADFVV F GLSGVQEV ...String:
MAGHSHRSSL KNGHKSYKSK HASKGALKRL YKGKVEKEPV GTGKPDKQVS KLQRKNKAKQ LRAQRILDSI ENRKLFEGKN GAAKIITIV PLVNDLDPLD ILYKLLKCAD DEGIMVQEVD SKRIFNVHIK KFKSNLKIII PDMTNFLNIL DCAKVADFVV F GLSGVQEV DEEFGEQIIR ALELQGIASY IGVISNLSAV HEKEKFQLDV KQSLESYFKH FFPSEERVYN LEKNSDALNV LR TLCQRLP RSINWRDNRG YVVADFVDFV ETSPDSGDLV IEGTVRGIGF NANRLVHIPD FGDFQLNKIE KISESSQKRK IIK EKATDS LSLELDLQTV FESNMNRDTL DEYAPEGTED WSDYDEDFEY DGLTTARYDD HGFLPGREQT SKKAAVPKGT SDYQ AKWYL DDVIDANEEE EAEQTNGKDE TMMEIDDEMM VEQDNEEVAG DEEYDIEDNE GFEELSPEEE ERQLREFRDM EKEDR EFPD EIELEPSESA IERLKRYRGL KNLYNCDWQV DEKDPSSPAE WKRLLRIGNY KNTKNRIIKE TKNEAQAIAG DRIRMF IRF PKFLLEKIQD PKQLLFAVYG LLLHEHKNAV VNFSLQRWEQ YDKPVPSQEP IVVQYGVRRY TIQPLFSQGS NSPNNVH KY ERFLHPDTVS VATCIAPVDF TQSPAIFFKP SPTDAKNIEL IGHGTFLNAD HSRILAKRAI LTGHPFRFHK TVVTVRYM F FRPEDVEWFK SIPLFTKSGR SGFIKESLGT HGYFKATFDG KLSAQDVVAM SLYKRMWPMP SLPWNGM

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Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER / Details: Relion
Final angle assignmentType: OTHER / Details: Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39865
FSC plot (resolution estimation)

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