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- EMDB-24286: State E2 nucleolar 60S ribosome biogenesis intermediate - Foot re... -

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Basic information

Entry
Database: EMDB / ID: EMD-24286
TitleState E2 nucleolar 60S ribosome biogenesis intermediate - Foot region map
Map dataState E2 foot region locally refined map
Sample
  • Complex: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4
    • RNA: x 3 types
    • Protein or peptide: x 16 types
Function / homology
Function and homology information


snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome ...snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / 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 / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / small-subunit processome / proteasome complex / protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / nuclear envelope / cytoplasmic translation / cytosolic large ribosomal subunit / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis protein 15, RNA recognition motif / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / Domain of unknown function (DUF4217) / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain ...Ribosome biogenesis protein 15, RNA recognition motif / DDX18/Has1, DEAD-box helicase domain / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Domain of unknown function DUF4217 / Domain of unknown function (DUF4217) / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / Pescadillo / Pescadillo N-terminus / BRCT domain, a BRCA1 C-terminus domain / 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. / breast cancer carboxy-terminal domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L7A/L8 / Ribosomal protein L15e, conserved site / Ribosomal protein L36e signature. / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal L15 / Ribosomal protein L1p/L10e family / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / BRCT domain profile. / BRCT domain / Ribosomal protein L15e signature. / DEAD/DEAH box helicase / BRCT domain superfamily / DEAD/DEAH box helicase domain / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / helicase superfamily c-terminal domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L23 / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein L23/L15e core domain superfamily / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL8A / Proteasome-interacting protein CIC1 / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / Pescadillo homolog / Ribosome biogenesis protein 15 / ATP-dependent RNA helicase HAS1 ...Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL8A / Proteasome-interacting protein CIC1 / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / Pescadillo homolog / Ribosome biogenesis protein 15 / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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 23, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24286.png

Downloads & links

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Map

FileDownload / File: emd_24286.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState E2 foot region locally refined map
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05132839 - 0.11928569
Average (Standard dev.)2.3413188e-05 (±0.0021613527)
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 foot region locally refined half map 1

Fileemd_24286_half_map_1.map
AnnotationState E2 foot region locally refined half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State E2 foot region locally refined half map 2

Fileemd_24286_half_map_2.map
AnnotationState E2 foot region locally refined 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: ITS-2
    • Protein or peptide: ATP-dependent RNA helicase HAS1
    • Protein or peptide: 60S ribosomal protein L8-ARibosome
    • Protein or peptide: Proteasome-interacting protein CIC1
    • Protein or peptide: Pescadillo homolog
    • Protein or peptide: Ribosome biogenesis protein 15
    • Protein or peptide: Ribosome biogenesis protein RLP7
    • Protein or peptide: 60S ribosomal protein L25
    • Protein or peptide: Ribosome biogenesis protein ERB1
    • RNA: 25S rRNA
    • Protein or peptide: Nucleolar protein 16Nucleolus
    • RNA: 5.8S rRNA5.8S ribosomal RNA
    • Protein or peptide: 60S ribosomal protein L15-ARibosome
    • Protein or peptide: 60S ribosomal protein L35
    • Protein or peptide: 60S ribosomal protein L27
    • Protein or peptide: 60S ribosomal protein L34-ARibosome
    • Protein or peptide: 60S ribosome biogenesis factor Spb1
    • Protein or peptide: 60S ribosomal protein L36-ARibosome
    • Protein or peptide: 60S ribosomal protein L13-ARibosome

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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-#19
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Molecular weightTheoretical: 3.3 MDa

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Macromolecule #1: ITS-2

MacromoleculeName: ITS-2 / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 27.786307 KDa
SequenceString:
CCUUCUCAAA CAUUCUGUUU GGUAGUGAGU GAUACUCUUU GGAGUUAACU UGAAAUUGCU GGCCUUUAGG CGAACAAUGU UCUUAAA

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Macromolecule #10: 25S rRNA

MacromoleculeName: 25S rRNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 95.192117 KDa
SequenceString: GUUUGACCUC AAAUCAGGUA GGAAAGCUCA AAUUUGAAAU CUGGUACCUU CGGUGCCCGA GUUGUAAUUU GGAGAGGGCA ACUUUGGGU UUGUAAAGUG CCUUCGAAGA GUCGCUAAGU GGGUGGUCCA UCUAAAGCUA AUAGUCGAUC CUAAGAGAUG G GGAAGCUC ...String:
GUUUGACCUC AAAUCAGGUA GGAAAGCUCA AAUUUGAAAU CUGGUACCUU CGGUGCCCGA GUUGUAAUUU GGAGAGGGCA ACUUUGGGU UUGUAAAGUG CCUUCGAAGA GUCGCUAAGU GGGUGGUCCA UCUAAAGCUA AUAGUCGAUC CUAAGAGAUG G GGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCUUC CGGAACCUGG AUAUGGAUUC UU CACACUG AAUGUGGAGA AAAUCCACAG GAAGGAAUAG UUUUCAUGCC AGGUCGUA

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Macromolecule #12: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 18.22373 KDa
SequenceString:
UGAACGCACA UUGCGCCCCU UGGUAUUCCA GGGGGCAUGC CUGUUUGAGC GUCAUUU

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Macromolecule #2: ATP-dependent RNA helicase HAS1

MacromoleculeName: ATP-dependent RNA helicase HAS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 56.798348 KDa
SequenceString: MATPSNKRSR DSESTEEPVV DEKSTSKQNN AAPEGEQTTC VEKFEELKLS QPTLKAIEKM GFTTMTSVQA RTIPPLLAGR DVLGAAKTG SGKTLAFLIP AIELLHSLKF KPRNGTGIIV ITPTRELALQ IFGVARELME FHSQTFGIVI GGANRRQEAE K LMKGVNML ...String:
MATPSNKRSR DSESTEEPVV DEKSTSKQNN AAPEGEQTTC VEKFEELKLS QPTLKAIEKM GFTTMTSVQA RTIPPLLAGR DVLGAAKTG SGKTLAFLIP AIELLHSLKF KPRNGTGIIV ITPTRELALQ IFGVARELME FHSQTFGIVI GGANRRQEAE K LMKGVNML IATPGRLLDH LQNTKGFVFK NLKALIIDEA DRILEIGFED EMRQIIKILP NEDRQSMLFS ATQTTKVEDL AR ISLRPGP LFINVVPETD NSTADGLEQG YVVCDSDKRF LLLFSFLKRN QKKKIIVFLS SCNSVKYYAE LLNYIDLPVL ELH GKQKQQ KRTNTFFEFC NAERGILICT DVAARGLDIP AVDWIIQFDP PDDPRDYIHR VGRTARGTKG KGKSLMFLTP NELG FLRYL KASKVPLNEY EFPENKIANV QSQLEKLIKS NYYLHQTAKD GYRSYLQAYA SHSLKTVYQI DKLDLAKVAK SYGFP VPPK VNITIGASGK TPNTKRRKTH K

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Macromolecule #3: 60S ribosomal protein L8-A

MacromoleculeName: 60S ribosomal protein L8-A / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: Proteasome-interacting protein CIC1

MacromoleculeName: Proteasome-interacting protein CIC1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 42.596691 KDa
SequenceString: MAKKSNSKKS TPVSTPSKEK KKVIEKKSST AIPRERVIKA VNELIKFTSK PQDENNEEGN NGKKNLLEDD EEELKKDLQL IVVNNKSFT GTSKSFKLKL LNVKHSFYKP WKEASATAVK DFKVLLILKD SDIKKVSEDD LFDQLDSEGI KVDEIICGKD L KTVYKAYE ...String:
MAKKSNSKKS TPVSTPSKEK KKVIEKKSST AIPRERVIKA VNELIKFTSK PQDENNEEGN NGKKNLLEDD EEELKKDLQL IVVNNKSFT GTSKSFKLKL LNVKHSFYKP WKEASATAVK DFKVLLILKD SDIKKVSEDD LFDQLDSEGI KVDEIICGKD L KTVYKAYE ARNAFISQFS LILADDSIVT SLPKLMGGKA YNKVETTPIS IRTHANKEFS LTTLTNNIKK VYMNQLPVKL PR GTTLNVH LGNLEWLRPE EFVDNVELIS EQLIKAYQIR SIFIKTNRSP VLPLYYNQDV LDELEAKKDK IEETHEDDMV TID GVQVHL STFNKGLMEI ANPSELGSIF SKQINNAKKR SSSELEKESS ESEAVKKAKS

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Macromolecule #5: Pescadillo homolog

MacromoleculeName: Pescadillo homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 69.984148 KDa
SequenceString: MRIKKKNTRG NARNFITRSQ AVRKLQVSLA DFRRLCIFKG IYPREPRNKK KANKGSTAPT TFYYAKDIQY LMHEPVLAKF REHKTFARK LTRALGRGEV SSAKRLEENR DSYTLDHIIK ERYPSFPDAI RDIDDALNML FLFSNLPSTN QVSSKIINDA Q KICNQWLA ...String:
MRIKKKNTRG NARNFITRSQ AVRKLQVSLA DFRRLCIFKG IYPREPRNKK KANKGSTAPT TFYYAKDIQY LMHEPVLAKF REHKTFARK LTRALGRGEV SSAKRLEENR DSYTLDHIIK ERYPSFPDAI RDIDDALNML FLFSNLPSTN QVSSKIINDA Q KICNQWLA YVAKERLVRK VFVSIKGVYY QANIKGEEVR WLVPFKFPEN IPSDVDFRIM LTFLEFYSTL LHFVLYKLYT DS GLIYPPK LDLKKDKIIS GLSSYILESR QEDSLLKLDP TEIEEDVKVE SLDASTLKSA LNADEANTDE TEKEEEQEKK QEK EQEKEQ NEETELDTFE DNNKNKGDIL IQPSKYDSPV ASLFSAFVFY VSREVPIDIL EFLILSCGGN VISEAAMDQI ENKK DIDMS KVTHQIVDRP VLKNKVAGRT YIQPQWIFDC INKGELVPAN KYLPGEALPP HLSPWGDAIG YDPTAPVEEG EEEES ESES ESEDQVEEED QEVVAGEEDD DDDEELQAQK ELELEAQGIK YSETSEADKD VNKSKNKKRK VDEEEEEKKL KMIMMS NKQ KKLYKKMKYS NAKKEEQAEN LKKKKKQIAK QKAKLNKLDS KK

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Macromolecule #6: Ribosome biogenesis protein 15

MacromoleculeName: Ribosome biogenesis protein 15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 25.499186 KDa
SequenceString: MVKSTSKTST KETVTKQPTE EKPIQEKEEL ALETSSSSSD EEDEKDEDEI EGLAASDDEQ SGTHKIKRLN PKKQANEKKS KDKKTLEEY SGIIYVSRLP HGFHEKELSK YFAQFGDLKE VRLARNKKTG NSRHYGFLEF VNKEDAMIAQ ESMNNYLLMG H LLQVRVLP ...String:
MVKSTSKTST KETVTKQPTE EKPIQEKEEL ALETSSSSSD EEDEKDEDEI EGLAASDDEQ SGTHKIKRLN PKKQANEKKS KDKKTLEEY SGIIYVSRLP HGFHEKELSK YFAQFGDLKE VRLARNKKTG NSRHYGFLEF VNKEDAMIAQ ESMNNYLLMG H LLQVRVLP KGAKIEKLYK YKKRVLVEKG ITKPVKQLKD NMKQKHEERI KKLAKSGIEF KW

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Macromolecule #7: Ribosome biogenesis protein RLP7

MacromoleculeName: Ribosome biogenesis protein RLP7 / type: protein_or_peptide / ID: 7 / 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

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Macromolecule #8: 60S ribosomal protein L25

MacromoleculeName: 60S ribosomal protein L25 / type: protein_or_peptide / ID: 8 / 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

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Macromolecule #9: Ribosome biogenesis protein ERB1

MacromoleculeName: Ribosome biogenesis protein ERB1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 91.830609 KDa
SequenceString: MMAKNNKTTE AKMSKKRAAS EESDVEEDED KLLSVDGLID AEASESDEDD DEYESAVEEK ESSSDKEAQD DSDDDSDAEL NKLLAEEEG DGEEDYDSSE FSDDTTSLTD RLSGVKLQTI VDPNIYSKYA DGSDRIIKPE INPVYDSDDS DAETQNTIGN I PLSAYDEM ...String:
MMAKNNKTTE AKMSKKRAAS EESDVEEDED KLLSVDGLID AEASESDEDD DEYESAVEEK ESSSDKEAQD DSDDDSDAEL NKLLAEEEG DGEEDYDSSE FSDDTTSLTD RLSGVKLQTI VDPNIYSKYA DGSDRIIKPE INPVYDSDDS DAETQNTIGN I PLSAYDEM PHIGYDINGK RIMRPAKGSA LDQLLDSIEL PEGWTGLLDK NSGSSLNLTK EELELISKIQ RNEQTDDSIN PY EPLIDWF TRHEEVMPLT AVPEPKRRFV PSKNEAKRVM KIVRAIREGR IIPPKKLKEM KEKEKIENYQ YDLWGDSTET NDH VMHLRA PKLPPPTNEE SYNPPEEYLL SPEEKEAWEN TEYSERERNF IPQKYSALRK VPGYGESIRE RFERSLDLYL APRV RKNKL NIDPNSLIPE LPSPKDLRPF PIRCSTIYAG HKGKVRTLSI DPSGLWLATG SDDGTVRVWE ILTGREVYRT TLIDD EENP DYHIECIEWN PDANNGILAV AVGENIHLIV PPIFGYDIEN NGKTKIEDGF GYDTFGTVKK SNLEVNENGD GDEDGE NES AKNAVKKQVA QWNKPSQKQL EKDICITISC KKTVKKLSWH RKGDYFVTVQ PDSGNTSVLI HQVSKHLTQS PFKKSKG II MDAKFHPFKP QLFVCSQRYV RIYDLSQQIL VKKLLPGARW LSKIDIHPRG DNLIASSFDK RVLWHDLDLA STPYKTLR Y HEKAVRSVNF HKKLPLFSSA ADDGTIHVFH ATVYDDMMKN PMIVPLKKLT GHKVINSLGV LDAIWHPREA WLFSAGADN TARLWTT

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Macromolecule #11: Nucleolar protein 16

MacromoleculeName: Nucleolar protein 16 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 26.954447 KDa
SequenceString: MTSVRKRKMN RSSVGKATRR NKDKQRKINI QSNPIIAANW DYSLTMAQNY KKLGLRAKLQ TPAGGKEADL SKVVKRIPLT KPVLDEDED EDEGEDEQND YNAATVELDE NEIPEGGARI QRDKNGDVVR VVYGKKKNFD ADEDVNEIKA RDTTEETEVV K KLEELASR ...String:
MTSVRKRKMN RSSVGKATRR NKDKQRKINI QSNPIIAANW DYSLTMAQNY KKLGLRAKLQ TPAGGKEADL SKVVKRIPLT KPVLDEDED EDEGEDEQND YNAATVELDE NEIPEGGARI QRDKNGDVVR VVYGKKKNFD ADEDVNEIKA RDTTEETEVV K KLEELASR PVIRKERSQS EREEEWLEKL YKKHGDDYKK MFFDKKLNIY QQSEGDLKRR LLRWKKRNGI ASK

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Macromolecule #13: 60S ribosomal protein L15-A

MacromoleculeName: 60S ribosomal protein L15-A / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 24.482357 KDa
SequenceString: MGAYKYLEEL QRKKQSDVLR FLQRVRVWEY RQKNVIHRAA RPTRPDKARR LGYKAKQGFV IYRVRVRRGN RKRPVPKGAT YGKPTNQGV NELKYQRSLR ATAEERVGRR AANLRVLNSY WVNQDSTYKY FEVILVDPQH KAIRRDARYN WICDPVHKHR E ARGLTATG ...String:
MGAYKYLEEL QRKKQSDVLR FLQRVRVWEY RQKNVIHRAA RPTRPDKARR LGYKAKQGFV IYRVRVRRGN RKRPVPKGAT YGKPTNQGV NELKYQRSLR ATAEERVGRR AANLRVLNSY WVNQDSTYKY FEVILVDPQH KAIRRDARYN WICDPVHKHR E ARGLTATG KKSRGINKGH KFNNTKAGRR KTWKRQNTLS LWRYRK

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Macromolecule #14: 60S ribosomal protein L35

MacromoleculeName: 60S ribosomal protein L35 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 2.165599 KDa
SequenceString:
GKKYQPKVTE KQRKKQIA

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Macromolecule #15: 60S ribosomal protein L27

MacromoleculeName: 60S ribosomal protein L27 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 1.801269 KDa
SequenceString:
LKVTKKHGAK KVAKRT

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Macromolecule #16: 60S ribosomal protein L34-A

MacromoleculeName: 60S ribosomal protein L34-A / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 4.511246 KDa
SequenceString:
FRRRNHVKKL ATISTLRPRQ YATVSKTHKT ALQAYGGSR

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Macromolecule #17: 60S ribosome biogenesis factor Spb1

MacromoleculeName: 60S ribosome biogenesis factor Spb1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 8.182842 KDa
SequenceString:
MIKDKDSAAD ADDLESELNA MYSDYKTRRS ERDAKFRVDE GFNRYTFRDT ENLPDWFLED EKEHSKIN

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Macromolecule #18: 60S ribosomal protein L36-A

MacromoleculeName: 60S ribosomal protein L36-A / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 11.151259 KDa
SequenceString:
MTVKTGIAIG LNKGKKVTSM TPAPKISYKK GAASNRTKFV RSLVREIAGL SPYERRLIDL IRNSGEKRAR KVAKKRLGSF TRAKAKVEE MNNIIAASRR H

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Macromolecule #19: 60S ribosomal protein L13-A

MacromoleculeName: 60S ribosomal protein L13-A / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741
Molecular weightTheoretical: 22.604164 KDa
SequenceString: MAISKNLPIL KNHFRKHWQE RVKVHFDQAG KKVSRRNARA TRAAKIAPRP LDLLRPVVRA PTVKYNRKVR AGRGFTLAEV KAAGLTAAY ARTIGIAVDH RRQNRNQEIF DANVQRLKEY QSKIIVFPRN GKAPEAEQVL SAAATFPIAQ PATDVEARAV Q DNGESAFR ...String:
MAISKNLPIL KNHFRKHWQE RVKVHFDQAG KKVSRRNARA TRAAKIAPRP LDLLRPVVRA PTVKYNRKVR AGRGFTLAEV KAAGLTAAY ARTIGIAVDH RRQNRNQEIF DANVQRLKEY QSKIIVFPRN GKAPEAEQVL SAAATFPIAQ PATDVEARAV Q DNGESAFR TLRLARSEKK FRGIREKRAR EKAEAEAEKK K

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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 chlorideSodium Chloride
10.0 mMMgCl2Magnesium Chloride
1.0 mMC9H15O6PHClTCEP
0.01 mMNP-40
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.30000000000000004 nm / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
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

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 118000 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 198000
FSC plot (resolution estimation)

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