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- EMDB-24270: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 l... -

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Basic information

Entry
Database: EMDB / ID: EMD-24270
TitleState E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model
Map dataState E2 Spb4 map
Sample
  • Complex: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
    • RNA: x 2 types
    • Protein or peptide: x 24 types
  • Ligand: x 1 types
Keywordsribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME
Function / homology
Function and homology information


: / Noc1p-Noc2p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane ...: / Noc1p-Noc2p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribonucleoprotein complex binding / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / maturation of LSU-rRNA / Transferases; Transferring one-carbon groups; Methyltransferases / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maintenance of translational fidelity / rRNA processing / transcription corepressor activity / ribosome biogenesis / ribosomal large subunit assembly / histone binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / hydrolase activity / structural constituent of ribosome / translation / GTPase activity / GTP binding / nucleolus / negative regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Nucleolar protein 12 / Nucleolar protein 12 (25kDa) / Nucleolar complex protein 2 / Noc2p family / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / WD repeat WDR12/Ytm1 / Ribosomal RNA methyltransferase, SPB1-like, C-terminal / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 ...Nucleolar protein 12 / Nucleolar protein 12 (25kDa) / Nucleolar complex protein 2 / Noc2p family / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / WD repeat WDR12/Ytm1 / Ribosomal RNA methyltransferase, SPB1-like, C-terminal / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / AdoMet-dependent rRNA methyltransferase SPB1-like / Spb1 C-terminal domain / Ribosomal RNA methyltransferase Spb1, DUF3381 / Ribosomal RNA large subunit methyltransferase E / Domain of unknown function DUF4217 / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / NLE / NLE (NUC135) domain / CCAAT-binding factor / CBF/Mak21 family / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / GTP binding domain / metallochaperone-like domain / TRASH domain / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7A/L8 / Ribosomal protein L30/YlxQ / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37ae/L37e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
RPL38 isoform 1 / Ribosome biogenesis protein RLP24 / RRP17 isoform 1 / AdoMet-dependent rRNA methyltransferase SPB1 / Ribosome biogenesis protein YTM1 / NOC2 isoform 1 / Ribosome biogenesis protein RLP7 / Nucleolar complex-associated protein 3 / 60S ribosomal protein L8 / SPB4 isoform 1 ...RPL38 isoform 1 / Ribosome biogenesis protein RLP24 / RRP17 isoform 1 / AdoMet-dependent rRNA methyltransferase SPB1 / Ribosome biogenesis protein YTM1 / NOC2 isoform 1 / Ribosome biogenesis protein RLP7 / Nucleolar complex-associated protein 3 / 60S ribosomal protein L8 / SPB4 isoform 1 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL22A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL34A / Nucleolar GTP-binding protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsCruz VE / Sekulski K / Peddada N / Erzberger JP
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135617-01 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150074 United States
Robert A. Welch FoundationI-1897 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Authors: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger /
Abstract: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.
History
DepositionJun 21, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24270.png

Downloads & links

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Map

FileDownload / File: emd_24270.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState E2 Spb4 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 420 pix.
= 453.6 Å		1.08 Å/pix.
x 420 pix.
= 453.6 Å		1.08 Å/pix.
x 420 pix.
= 453.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.08939699 - 0.1515478
Average (Standard dev.)0.000054562894 (±0.0031867602)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 453.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: State E2 Spb4 local half map 1

Fileemd_24270_half_map_1.map
AnnotationState E2 Spb4 local half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State E2 Spb4 local half map 2

Fileemd_24270_half_map_2.map
AnnotationState E2 Spb4 local half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.

EntireName: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
Components
  • Complex: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
    • RNA: 25S rRNA
    • RNA: 5.8S rRNA
    • Protein or peptide: RRP17 isoform 1
    • Protein or peptide: NOC2 isoform 1
    • Protein or peptide: 60S ribosomal protein L3
    • Protein or peptide: RPL8A isoform 1
    • Protein or peptide: NOC3 isoform 1
    • Protein or peptide: 60S ribosomal protein L17-A
    • Protein or peptide: 60S ribosomal protein L19-A
    • Protein or peptide: 60S ribosomal protein L22-A
    • Protein or peptide: 60S ribosomal protein L23-A
    • Protein or peptide: 60S ribosomal protein L25
    • Protein or peptide: 60S ribosomal protein L27-A
    • Protein or peptide: Nucleolar GTP-binding protein 1
    • Protein or peptide: 60S ribosomal protein L30
    • Protein or peptide: 60S ribosomal protein L31-A
    • Protein or peptide: 60S ribosomal protein L34-A
    • Protein or peptide: RPL38 isoform 1
    • Protein or peptide: Ribosome biogenesis protein ERB1
    • Protein or peptide: Pescadillo homolog
    • Protein or peptide: YTM1 isoform 1
    • Protein or peptide: RLP7 isoform 1
    • Protein or peptide: Ribosome biogenesis protein RLP24
    • Protein or peptide: SPB1 isoform 1
    • Protein or peptide: 60S ribosomal protein L37-A
    • Protein or peptide: SPB4 isoform 1
  • Ligand: ZINC ION

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Supramolecule #1: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.

SupramoleculeName: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 3.3 MDa

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Macromolecule #1: 25S rRNA

MacromoleculeName: 25S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 225.356453 KDa
SequenceString: AUGCCUGAAU AGGGUGAAGC CAGAGGAAAC UCUGGUGGAG GCUCGCGAAU UUGGGUAUAG UAGCAAAUAU UCAAAUGAGA ACUUUGAAG ACUGAAGUGG GGAAAGGUUC CACGUCAACA GCAGUUGGAC GUGGGUUAGU CGAUCCUAAG AGAUGGUUUC A AAGGCCUG ...String:
AUGCCUGAAU AGGGUGAAGC CAGAGGAAAC UCUGGUGGAG GCUCGCGAAU UUGGGUAUAG UAGCAAAUAU UCAAAUGAGA ACUUUGAAG ACUGAAGUGG GGAAAGGUUC CACGUCAACA GCAGUUGGAC GUGGGUUAGU CGAUCCUAAG AGAUGGUUUC A AAGGCCUG ACAGGCCACC AUCGAAAGGG AAUCCGGUUA AGAUUCCGGA ACCUGGAUAU GGAUUCUUCA CGGUAACGUA AC UGAAUGU GGAGACGUCG GCGCGAGCCC UGGGAGGAGU UAUCUUUUCU UCUUAACAGC UUAUCACCCC GGAAUUGGUU UAU CCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCA CAGGA AGGAAUAGUU UUCAUGCCAG GUCGUACUGU CUCCAAGGUG AACAGCCUCU AGUUGAUAGA AGAUAAGGGA AGUCG GUCC GUAACUUCGG GAUAAGGAUU GGCUCUAAGG GUCGGGUAGU GAGGGCCUUG GUCACGGCCU UGGCUUGCUA CAAUUA ACG AUCAACUUAG AACUGGUACG GACAAGGGGA AUCUGACUGU UAACGAGAUU CCCACUGUCC CUAUCUACUA UCUAGCG AG GCUGUCUGAU CAGGCAUUGC GUAAGCAGUA GAGUAGCCGU UACGAUCUGC UGAGA

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Macromolecule #2: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 23.067643 KDa
SequenceString:
GAACGCGCGA UACUCUUUGA ACGCACAUUG CGCCCCUUGG UAUUCCAGGG GGCAUCUUUG AAAGCGUAUU GC

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Macromolecule #3: RRP17 isoform 1

MacromoleculeName: RRP17 isoform 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 28.032553 KDa
SequenceString: MAVHTNRQIL TRGKNYATKQ SKKFGTDEVT FDKDSRLDYL TGFHKRKLQR QKKAQEFIKE QERLRKIEER QKIRQERKEV MEEQLKTFK ESLNLEAEIE DAKNDKTEDL QVESDESWHG FDSDKDDGDN DNNESSVKPI LKKGAITEIY DDSTTVELET L EPNDNFEY ...String:
MAVHTNRQIL TRGKNYATKQ SKKFGTDEVT FDKDSRLDYL TGFHKRKLQR QKKAQEFIKE QERLRKIEER QKIRQERKEV MEEQLKTFK ESLNLEAEIE DAKNDKTEDL QVESDESWHG FDSDKDDGDN DNNESSVKPI LKKGAITEIY DDSTTVELET L EPNDNFEY LAQLNNVKLE KAEKVLKQSI NRATKYAKFL GVDEKQKKKP RVKKFRYLTK NERRINQRKA NDNKRRR

UniProtKB: RRP17 isoform 1

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Macromolecule #4: NOC2 isoform 1

MacromoleculeName: NOC2 isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 81.719289 KDa
SequenceString: MGKVSKSTKK FQSKHLKHTL DQRRKEKIQK KRIQGRRGNK TDQEKADAAG TREQQQLKKS AKEEVFKDMS VETFFEKGIE IPKENKKLK KKTTKEQSDE DSSSSEEEED MGQSMAKLAE KDPEFYKYLE ENDKDLLDFA GTNPLDGIDS QDEGEDAERN S NIEEKSEQ ...String:
MGKVSKSTKK FQSKHLKHTL DQRRKEKIQK KRIQGRRGNK TDQEKADAAG TREQQQLKKS AKEEVFKDMS VETFFEKGIE IPKENKKLK KKTTKEQSDE DSSSSEEEED MGQSMAKLAE KDPEFYKYLE ENDKDLLDFA GTNPLDGIDS QDEGEDAERN S NIEEKSEQ MELEKEKIEL SLKLVRKWKK QLHDSPSLKL LRNIISAFKV AVNLNKEENI EDYKYAITDE KAFHELMFMV LK DVPQAIQ KMAPYKIVKG ARTLPNGGNV SRVSSIVKSH AGSLLILLND ITNTETAALV LHSVNELMPY LLSYRRILKE LIK SIVGVW STTRELETQI ASFAFLINTT KEFKKSMLET TLKTTYSTFI KSCRKTNMRS MPLINFQKNS AAELFGIDEV LGYQ VGFEY IRQLAIHLRN TMNATTKKSS KINSAEAYKI VYNWQFCHSL DFWSRVLSFA CQPEKENGSE SPLRQLIYPL VQVTL GVIR LIPTPQFFPL RFYLIKSLIR LSQNSGVFIP IYPLLSEILT STAFTKAPKK SPNLAAFDFE HNIKCTQAYL NTKIYQ EGL SEQFVDLLGD YFALYCKNIA FPELVTPVII SLRRYIKTST NVKLNKRLST VVEKLNQNST FIQEKRSDVE FGPTNKS EV SRFLNDVAWN KTPLGSYVAV QREVKEEKAR LMRESMEEQD KERETEEAKL LNSLESDDDN EDVEMSDA

UniProtKB: NOC2 isoform 1

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Macromolecule #5: 60S ribosomal protein L3

MacromoleculeName: 60S ribosomal protein L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 43.850793 KDa
SequenceString: MSHRKYEAPR HGHLGFLPRK RAASIRARVK AFPKDDRSKP VALTSFLGYK AGMTTIVRDL DRPGSKFHKR EVVEAVTVVD TPPVVVVGV VGYVETPRGL RSLTTVWAEH LSDEVKRRFY KNWYKSKKKA FTKYSAKYAQ DGAGIERELA RIKKYASVVR V LVHTQIRK ...String:
MSHRKYEAPR HGHLGFLPRK RAASIRARVK AFPKDDRSKP VALTSFLGYK AGMTTIVRDL DRPGSKFHKR EVVEAVTVVD TPPVVVVGV VGYVETPRGL RSLTTVWAEH LSDEVKRRFY KNWYKSKKKA FTKYSAKYAQ DGAGIERELA RIKKYASVVR V LVHTQIRK TPLAQKKAHL AEIQLNGGSI SEKVDWAREH FEKTVAVDSV FEQNEMIDAI AVTKGHGFEG VTHRWGTKKL PR KTHRGLR KVACIGAWHP AHVMWSVARA GQRGYHSRTS INHKIYRVGK GDDEANGATS FDRTKKTITP MGGFVHYGEI KND FIMVKG CIPGNRKRIV TLRKSLYTNT SRKALEEVSL KWIDTASKFG KGRFQTPAEK HAFMGTLKKD L

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #6: RPL8A isoform 1

MacromoleculeName: RPL8A isoform 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 28.17582 KDa
SequenceString: MAPGKKVAPA PFGAKSTKSN KTRNPLTHST PKNFGIGQAV QPKRNLSRYV KWPEYVRVQR QKKILSIRLK VPPTIAQFQY TLDRNTAAE TFKLFNKYRP ETAAEKKERL TKEAAAVAEG KSKQDASPKP YAVKYGLNHV VALIENKKAK LVLIANDVDP I ELVVFLPA ...String:
MAPGKKVAPA PFGAKSTKSN KTRNPLTHST PKNFGIGQAV QPKRNLSRYV KWPEYVRVQR QKKILSIRLK VPPTIAQFQY TLDRNTAAE TFKLFNKYRP ETAAEKKERL TKEAAAVAEG KSKQDASPKP YAVKYGLNHV VALIENKKAK LVLIANDVDP I ELVVFLPA LCKKMGVPYA IVKGKARLGT LVNQKTSAVA ALTEVRAEDE AALAKLVSTI DANFADKYDE VKKHWGGGIL GN KAQAKMD KRAKNSDSA

UniProtKB: 60S ribosomal protein L8

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Macromolecule #7: NOC3 isoform 1

MacromoleculeName: NOC3 isoform 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 75.689008 KDa
SequenceString: MAKRNRSQFR IQERTAKKRK HEDSLLEGNV FQNAPEDMDE NTIYSAKGSS WDEEEQDYEM VPRKNRSDTS NLVEGLPIKV NGKVERKLH KAQEKPKDDD EEDEDSNDSS EDDEGPNEEQ EAEAKEDEPD TEEKILQLKE DIADLVTKVM EEPEENTAAL G RLCKMVES ...String:
MAKRNRSQFR IQERTAKKRK HEDSLLEGNV FQNAPEDMDE NTIYSAKGSS WDEEEQDYEM VPRKNRSDTS NLVEGLPIKV NGKVERKLH KAQEKPKDDD EEDEDSNDSS EDDEGPNEEQ EAEAKEDEPD TEEKILQLKE DIADLVTKVM EEPEENTAAL G RLCKMVES KNPNTCKFSM LALVPVFKSI IPGYRIRPLT ETEKKEKVSK EVSKLRNFEQ ALVYNYKNYV GRLQSLSKTP SN AAPIQVS LGILATQAAK ELISTASHFN FRTDIFTLLL RRICKPRIST DPTSIQIIQT FETLLNEDEE GSISFEILRI FNK ILKTRN FNIEESVLNM LLSLDVLHDY DPNTKLKGNV SAPKLKKKDR VHLSKKQRKA RKEMQQIEEE MRNAEQAVSA EERE RNQSE ILKIVFTIYL NILKNNAKTL IGSVLEGLTK FGNMANFDLL GDFLEVMKEL ISDTEFDNLS SAEVRKALLC IVSAF SLIS NTQYMKVNVD LSKFVDGLYA LLPYICLDAD IELSYRSLRL ADPLNNEIIK PSVNVSTKAE LLLKALDHVF FRSKSG TKE RATAFTKRLY MCISHTPEKT SIAILKFIDK LMNRYPEISG LYSSEDRIGN GHFIMEADNP SRSNPEAATL WDNALLE KH YCPVVTKGLR SLSSRSKECS K

UniProtKB: Nucleolar complex-associated protein 3

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Macromolecule #8: 60S ribosomal protein L17-A

MacromoleculeName: 60S ribosomal protein L17-A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 20.589518 KDa
SequenceString:
MARYGATSTN PAKSASARGS YLRVSFKNTR ETAQAINGWE LTKAQKYLEQ VLDHQRAIPF RRFNSSIGRT AQGKEFGVTK ARWPAKSVK FVQGLLQNAA ANAEAKGLDA TKLYVSHIQV NQAPKQRRRT YRAHGRINKY ESSPSHIELV VTEKEEAVAK A AEKKVVRL TSRQRGRIAA QKRIAA

UniProtKB: Large ribosomal subunit protein uL22A

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Macromolecule #9: 60S ribosomal protein L19-A

MacromoleculeName: 60S ribosomal protein L19-A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 21.762316 KDa
SequenceString:
MANLRTQKRL AASVVGVGKR KVWLDPNETS EIAQANSRNA IRKLVKNGTI VKKAVTVHSK SRTRAHAQSK REGRHSGYGK RKGTREARL PSQVVWIRRL RVLRRLLAKY RDAGKIDKHL YHVLYKESKG NAFKHKRALV EHIIQAKADA QREKALNEEA E ARRLKNRA ARDRRAQRVA EKRDALLKED A

UniProtKB: Large ribosomal subunit protein eL19A

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Macromolecule #10: 60S ribosomal protein L22-A

MacromoleculeName: 60S ribosomal protein L22-A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 13.711359 KDa
SequenceString:
MAPNTSRKQK IAKTFTVDVS SPTENGVFDP ASYAKYLIDH IKVEGAVGNL GNAVTVTEDG TVVTVVSTAK FSGKYLKYLT KKYLKKNQL RDWIRFVSTK TNEYRLAFYQ VTPEEDEEED EE

UniProtKB: Large ribosomal subunit protein eL22A

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Macromolecule #11: 60S ribosomal protein L23-A

MacromoleculeName: 60S ribosomal protein L23-A / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 4.023917 KDa
SequenceString:
LPVGAIMNCA RNLYIIMATV KKGKPELRKK VMEDNA

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Macromolecule #12: 60S ribosomal protein L25

MacromoleculeName: 60S ribosomal protein L25 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 15.787612 KDa
SequenceString:
MAPSAKATAA KKAVVKGTNG KKALKVRTSA TFRLPKTLKL ARAPKYASKA VPHYNRLDSY KVIEQPITSE TAMKKVEDGN ILVFQVSMK ANKYQIKKAV KELYEVDVLK VNTLVRPNGT KKAYVRLTAD YDALDIANRI GYI

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #13: 60S ribosomal protein L27-A

MacromoleculeName: 60S ribosomal protein L27-A / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 15.56836 KDa
SequenceString:
MAKFLKAGKV AVVVRGRYAG KKVVIVKPHD EGSKSHPFGH ALVAGIERYP LKVTKKHGAK KVAKRTKIKP FIKVVNYNHL LPTRYTLDV EAFKSVVSTE TFEQPSQREE AKKVVKKAFE ERHQAGKNQW FFSKLRF

UniProtKB: Large ribosomal subunit protein eL27A

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Macromolecule #14: Nucleolar GTP-binding protein 1

MacromoleculeName: Nucleolar GTP-binding protein 1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 74.531227 KDa
SequenceString: MQLSWKDIPT VAPANDLLDI VLNRTQRKTP TVIRPGFKIT RIRAFYMRKV KYTGEGFVEK FEDILKGFPN INDVHPFHRD LMDTLYEKN HYKISLAAIS RAKSLVEQVA RDYVRLLKFG QSLFQCKQLK RAALGRMATI VKKLRDPLAY LEQVRQHIGR L PSIDPNTR ...String:
MQLSWKDIPT VAPANDLLDI VLNRTQRKTP TVIRPGFKIT RIRAFYMRKV KYTGEGFVEK FEDILKGFPN INDVHPFHRD LMDTLYEKN HYKISLAAIS RAKSLVEQVA RDYVRLLKFG QSLFQCKQLK RAALGRMATI VKKLRDPLAY LEQVRQHIGR L PSIDPNTR TLLICGYPNV GKSSFLRCIT KSDVDVQPYA FTTKSLYVGH FDYKYLRFQA IDTPGILDRP TEEMNNIEMQ SI YAIAHLR SCVLYFMDLS EQCGFTIEAQ VKLFHSIKPL FANKSVMVVI NKTDIIRPED LDEERAQLLE SVKEVPGVEI MTS SCQLEE NVMEVRNKAC EKLLASRIEN KLKSQSRINN VLNKIHVAQP QARDDVKRTP FIPESVKNLK KYDPEDPNRR KLAR DIEAE NGGAGVFNVN LKDKYLLEDD EWKNDIMPEI LDGKNVYDFL DPEIAAKLQA LEEEEEKLEN EGFYNSDDEE EIYDG FEAS EVDDIKEKAA WIRNRQKTMI AEARNRKSLK NKAIMPRSKL TKSFGKMEEH MSTLGHDMSA LQDKQNRAAR KNRYVE RGS DVVFGDQDAL TASTENGVKL RQTDRLLDGV ADGSMRSKAD RMAKMERRER NRHAKQGESD RHNAVSLSKH LFSGKRG VG KTDFR

UniProtKB: Nucleolar GTP-binding protein 1

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Macromolecule #15: 60S ribosomal protein L30

MacromoleculeName: 60S ribosomal protein L30 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 11.430364 KDa
SequenceString:
MAPVKSQESI NQKLALVIKS GKYTLGYKST VKSLRQGKSK LIIIAANTPV LRKSELEYYA MLSKTKVYYF QGGNNELGTA VGKLFRVGV VSILEAGDSD ILTTLA

UniProtKB: Large ribosomal subunit protein eL30

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Macromolecule #16: 60S ribosomal protein L31-A

MacromoleculeName: 60S ribosomal protein L31-A / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 12.980158 KDa
SequenceString:
MAGLKDVVTR EYTINLHKRL HGVSFKKRAP RAVKEIKKFA KLHMGTDDVR LAPELNQAIW KRGVKGVEYR LRLRISRKRN EEEDAKNPL FSYVEPVLVA SAKGLQTVVV EEDA

UniProtKB: Large ribosomal subunit protein eL31A

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Macromolecule #17: 60S ribosomal protein L34-A

MacromoleculeName: 60S ribosomal protein L34-A / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 13.673196 KDa
SequenceString:
MAQRVTFRRR NPYNTRSNKI KVVKTPGGIL RAQHVKKLAT RPKCGDCGSA LQGISTLRPR QYATVSKTHK TVSRAYGGSR CANCVKERI IRAFLIEEQK IVKKVVKEQT EAAKKSEKKA KK

UniProtKB: Large ribosomal subunit protein eL34A

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Macromolecule #18: RPL38 isoform 1

MacromoleculeName: RPL38 isoform 1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 8.845561 KDa
SequenceString:
MAREITDIKQ FLELTRRADV KTATVKINKK LNKAGKPFRQ TKFKVRGSSS LYTLVINDAG KAKKLIQSLP PTLKVNRL

UniProtKB: RPL38 isoform 1

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Macromolecule #19: Ribosome biogenesis protein ERB1

MacromoleculeName: Ribosome biogenesis protein ERB1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 48.685059 KDa
SequenceString: DHVMHLRAPK LPLDLYLAPR VRKNKLNIDP NSLIPELPSP KDLRPFPIRC STIYAGHKGK VRTLSIDPSG LWLATGSDDG TVRVWEILT GREVYRTTLI DPKDNPDYHI ECIEWNPDAN NGILAVAVGE NIHLIVPPIF GYDIENNGKT KIEDGFGYDT F GTVKKSNL ...String:
DHVMHLRAPK LPLDLYLAPR VRKNKLNIDP NSLIPELPSP KDLRPFPIRC STIYAGHKGK VRTLSIDPSG LWLATGSDDG TVRVWEILT GREVYRTTLI DPKDNPDYHI ECIEWNPDAN NGILAVAVGE NIHLIVPPIF GYDIENNGKT KIEDGFGYDT F GTVKKSNL EVNAIEWNPD ANNGILAKNA VKKQVAQWNK PSQKQLEKDI CITISCKKTV KKLSWHRKGD YFVTVQPDSG NT SVLIHQV SKHLTQSPFK KSKGIIMDAK FHPFKPQLFV CSQRYVRIYD LSQQILVKKL LPGARWLSKI DIHPRGDNLI ASS FDKRVL WHDLDLASTP YKTLRYHEKA VRSVNFHKKL PLFSSAADDG TIHVFHATVY DDMMKNPMIV PLKKLTGHKV INSL GVLDA IWHPREAWLF SAGADNTARL WTTI

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Macromolecule #20: Pescadillo homolog

MacromoleculeName: Pescadillo homolog / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 12.445749 KDa
SequenceString:
MRIKKKNTRG NARNFITRSQ AVRKLQVSLA DFRRLCIFKG IYPREPRNKK KANKGSTAPT TFYYAKDIQY EEKKLKMIMM SNKQKKLYK KMKYSNAKKE EQAEN

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Macromolecule #21: YTM1 isoform 1

MacromoleculeName: YTM1 isoform 1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 51.426637 KDa
SequenceString: MTEDKSQVKI RFFTREKDEL LHVQDTPMYA PISLKRYGLS EIVNHLLGSE KPVPFDFLIE GELLRTSLHD YLTKKGLSSE ASLNVEYTR AILPPSYLNS FSNEDWVSSL DVGDGSKHII SGSYDGIVRT WDLSGNVQKQ YSGHSGPIRA VKYISNTRLV S AGNDRTLR ...String:
MTEDKSQVKI RFFTREKDEL LHVQDTPMYA PISLKRYGLS EIVNHLLGSE KPVPFDFLIE GELLRTSLHD YLTKKGLSSE ASLNVEYTR AILPPSYLNS FSNEDWVSSL DVGDGSKHII SGSYDGIVRT WDLSGNVQKQ YSGHSGPIRA VKYISNTRLV S AGNDRTLR LWKTKNDDLK LTSQQQAQED DDDEVNIEDG KTLAILEGHK APVVSIDVSD NSRILSASYD NSIGFWSTIY KE MTVVDPL EDINNPNNKI STAARKRRKL TMKDGTIRRR APLSLLESHT APVEQVIFDS TDNTVGYSVS QDHTIKTWDL VTA RCIDTR TTSYSLLSIA QLSTLNLLAC GSSARHITLH DPRVGASSKV TQQQLIGHKN FVSSLDTCPE NEYILCSGSH DGTV KVWDV RSTSPMYTIT REDKSVQKGV NDKVFAVKWA EKVGIISAGQ DKKIQINKGD NIFKN

UniProtKB: Ribosome biogenesis protein YTM1

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Macromolecule #22: RLP7 isoform 1

MacromoleculeName: RLP7 isoform 1 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 36.621074 KDa
SequenceString: MSSTQDSKAQ TLNSNPEILL RKRRNADRTR IERQELAKKK REEQIKKKRS NKNKFVRAES IVAKTLATSR EKERIKRVSI LEDKKAKNE TQHIASGKDF ILKITEKANG AEENSVDLEE TEEEEDDGLI REKTTYDGKP ALLFIVRVRG PLAVNIPNKA F KILSLLRL ...String:
MSSTQDSKAQ TLNSNPEILL RKRRNADRTR IERQELAKKK REEQIKKKRS NKNKFVRAES IVAKTLATSR EKERIKRVSI LEDKKAKNE TQHIASGKDF ILKITEKANG AEENSVDLEE TEEEEDDGLI REKTTYDGKP ALLFIVRVRG PLAVNIPNKA F KILSLLRL VETNTGVFVK LTKNVYPLLK VIAPYVVIGK PSLSSIRSLI QKRGRIIYKG ENEAEPHEIV LNDNNIVEEQ LG DHGIICV EDIIHEIATM GESFSVCNFF LQPFKLNREV SGFGSLNRLR KIKQREAESR TRQFSNAATA PVIEVDIDSL LAK LN

UniProtKB: Ribosome biogenesis protein RLP7

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Macromolecule #23: Ribosome biogenesis protein RLP24

MacromoleculeName: Ribosome biogenesis protein RLP24 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 24.02765 KDa
SequenceString: MRIYQCHFCS SPCYPGHGIM FVRNDAKEFR FCRSKCHKAF KQRRNPRKLK WTKAFRKAAG KELAVDSTLT FAQRRNVPVR YNRELVATT LKAMARIEEI RQKRERAFYK NRMRGNKEKD FLRDKKLVES NPELLRIREV EIARKLAKEQ ERAESVSEQE E SEEEEEDM ...String:
MRIYQCHFCS SPCYPGHGIM FVRNDAKEFR FCRSKCHKAF KQRRNPRKLK WTKAFRKAAG KELAVDSTLT FAQRRNVPVR YNRELVATT LKAMARIEEI RQKRERAFYK NRMRGNKEKD FLRDKKLVES NPELLRIREV EIARKLAKEQ ERAESVSEQE E SEEEEEDM EIDSDEEEEE QLEKQKILLK NRRRNTKKIA F

UniProtKB: Ribosome biogenesis protein RLP24

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Macromolecule #24: SPB1 isoform 1

MacromoleculeName: SPB1 isoform 1 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 96.656172 KDa
SequenceString: MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV IDLCAAPGSW CQVASKLCPV NSLIIGVDIV PMKPMPNVI TFQSDITTED CRSKLRGYMK TWKADTVLHD GAPNVGLGWV QDAFTQSQLT LQALKLAVEN LVVNGTFVTK I FRSKDYNK ...String:
MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV IDLCAAPGSW CQVASKLCPV NSLIIGVDIV PMKPMPNVI TFQSDITTED CRSKLRGYMK TWKADTVLHD GAPNVGLGWV QDAFTQSQLT LQALKLAVEN LVVNGTFVTK I FRSKDYNK LIWVFQQLFE KVEATKPPAS RNVSAEIFVV CKGFKAPKRL DPRLLDPKEV FEELPDGQQN MESKIYNPEK KV RKRQGYE EGDNLLYHET SILDFVRTED PISMLGEMNK FTIDENDHEW KILKKLKQTT DEFRSCIEDL KVLGKKDFKM ILR WRKIAR EILGIEVKDD AKTEIEVVPL TEEEQIEKDL QGLQEKQRLN VKRERRRKNE MKQKELQRMQ MNMITPTDIG IEAA SLGKE SLFNLKTAEK TGILNDLAKG KKRMIFTDDE LAKDNDIYID ENIMIKDKDS AADADDLESE LNAMYSDYKT RRSER DAKF RAKQARGGDN EEEWTGFNEG SLEKKEEEGK DYIEDNDDEG VEGDSDDDEA ITNLISKLKG QEGDHKLSSK ARMIFN DPI FNNVEPDLPV NTVNDGIMSS ESVGDISKLN KKRKHEEMHQ KQDEADSSDE SSSDDSDFEI VANDNASEEF DSDYDSE EE KNQTKKEKHS RDIDIATVEA MTLAHQLALG QKNKHDLVDE GFNRYTFRDT ENLPDWFLED EKEHSKINKP ITKEAAMA I KEKIKAMNAR PIKKVAEAKA RKRMRAVARL EKIKKKAGLI NDDSDKTEKD KAEEISRLMR KVTKKPKTKP KVTLVVASG RNKGLAGRPK GVKGKYKMVD GVMKNEQRAL RRIAKKHHKK K

UniProtKB: AdoMet-dependent rRNA methyltransferase SPB1

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Macromolecule #25: 60S ribosomal protein L37-A

MacromoleculeName: 60S ribosomal protein L37-A / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 9.877395 KDa
SequenceString:
MGKGTPSFGK RHNKSHTLCN RCGRRSFHVQ KKTCSSCGYP AAKTRSYNWG AKAKRRHTTG TGRMRYLKHV SRRFKNGFQT GSASKASA

UniProtKB: Large ribosomal subunit protein eL37A

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Macromolecule #26: SPB4 isoform 1

MacromoleculeName: SPB4 isoform 1 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 69.492172 KDa
SequenceString: MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD SVTGSGKTAA FVIPVLEKVV KEEANTSKFK KAHFHSLII APTRELSRQI ESVVLSFLEH YPSDLFPIKC QLLVGTNEAT VRDDVSNFLR NRPQILIGTP GRVLDFLQMP A VKTSACSM ...String:
MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD SVTGSGKTAA FVIPVLEKVV KEEANTSKFK KAHFHSLII APTRELSRQI ESVVLSFLEH YPSDLFPIKC QLLVGTNEAT VRDDVSNFLR NRPQILIGTP GRVLDFLQMP A VKTSACSM VVMDEADRLL DMSFIKDTEK ILRLLPKQRR TGLFSATMRS AGSDIFKTGL RNPVRITVNS KNQAPSSLKL NY CVVNPAE KLQLLVSILN NYKFKKCIVY FPTCVSVSYF YSFIQYLGKR NILVNEVEIF SLHGKLQTSA RTKTLTAFTD SLS NSVLFT TDVAARGIDI PDVDLVIQLD PPTNTDMFMH RCGRTGRANR VGKAITFLNE GREEDFIPFM QVKNVELEEL DLEV KGITA NFYEDFRNWI LEDRDRFDKG VKAYVAFIKY YSNHSATSIF RLQSLDYVGI AKLYGLFRLP RMPEITKYLA TEKQE GIFP GNWLVDPPVN MDEYKYKDKK REKERQETLK NISLINDKKK LKSELKKKNL AWSDKTLTKE RKLERKEKMS LKRKAI EEE LKAEELDENA EEERIKEDWK EIVLQNKRKK VSSKAIQGNF DDL

UniProtKB: SPB4 isoform 1

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Macromolecule #27: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 27 / 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

Concentration0.45 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMCH2[CH2NHC(CH2OH)3]2Bis-Tris-Propane
150.0 mMNaClSodium Chloride
10.0 mMMgCl2Magnesium Chloride
1.0 mMC9H15O6PHClTCEP
0.01 % (w/v)NP-40
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4523 / Average exposure time: 0.05 sec. / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 825096
Startup modelType of model: EMDB MAP
EMDB ID:

3891

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 198000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 118000 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7nad:
State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model

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