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- EMDB-53201: Yeast pre-60S Domain II intermediate -

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Basic information

Entry
Database: EMDB / ID: EMD-53201
TitleYeast pre-60S Domain II intermediate
Map data
Sample
  • Complex: Yeast pre-60S Domain II
    • Protein or peptide: x 14 types
    • RNA: x 2 types
KeywordspreLSU / preribosome / complex / Noc2-TAP particle / RIBOSOME
Function / homology
Function and homology information


Noc1p-Noc2p complex / Noc2p-Noc3p complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Noc1p-Noc2p complex / Noc2p-Noc3p complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / preribosome, large subunit precursor / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / rRNA processing / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / ribosome / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nop4, RNA recognition motif 1 / Nop4, RNA recognition motif 2 / Nop4, RNA recognition motif 3 / Nop4, RNA recognition motif 4 / CEBPZ/Mak21-like / : / Nucleolar complex protein 2 / Noc2p family / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 ...Nop4, RNA recognition motif 1 / Nop4, RNA recognition motif 2 / Nop4, RNA recognition motif 3 / Nop4, RNA recognition motif 4 / CEBPZ/Mak21-like / : / Nucleolar complex protein 2 / Noc2p family / Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / Mak16 protein / Mak16 protein C-terminal region / CCAAT-binding factor / CBF/Mak21 family / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L35Ae signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L18e / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae / Ribosomal protein L32e signature. / Ribosomal protein L35A superfamily / Ribosomal protein L14 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Armadillo-type fold / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL30A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / Large ribosomal subunit protein eL14A / Nucleolar protein 4 ...Large ribosomal subunit protein uL30A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL4A / Protein MAK16 / Large ribosomal subunit protein uL13A / Ribosomal RNA-processing protein 1 / Large ribosomal subunit protein eL14A / Nucleolar protein 4 / Large ribosomal subunit protein eL32 / Nucleolar complex protein 2 / Large ribosomal subunit protein eL6A / Ribosome biogenesis protein MAK21
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGrundmann L / Gerhalter M / Prattes M / Grishkovskaya I / Kotisch H / Haselbach D / Bergler H
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundPAT1908524 Austria
CitationJournal: To Be Published
Title: A comprehensive view on r- protein binding and rRNA domain structuring during early ribosome formation
Authors: Gerhalter M / Prattes M / Grundmann L / Grishkovskaya I / Semarari EF / Zisser G / Harald K / Merl-Pharm J / Hauck SM / Haselbach D / Bergler H
History
DepositionMar 19, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53201.png

Downloads & links

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Map

FileDownload / File: emd_53201.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 440 pix.
= 402.03 Å		0.91 Å/pix.
x 440 pix.
= 402.03 Å		0.91 Å/pix.
x 440 pix.
= 402.03 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9137 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0981
Minimum - Maximum-0.01978551 - 2.420328
Average (Standard dev.)0.0013186795 (±0.024952425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 402.03 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53201_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_53201_half_map_2.map
Projections & Slices
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Sample components

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Entire : Yeast pre-60S Domain II

EntireName: Yeast pre-60S Domain II
Components
  • Complex: Yeast pre-60S Domain II
    • Protein or peptide: Ribosome biogenesis protein MAK21
    • Protein or peptide: Nucleolar complex protein 2
    • Protein or peptide: 60S ribosomal protein L4-A
    • Protein or peptide: Protein MAK16
    • Protein or peptide: 60S ribosomal protein L6-A
    • Protein or peptide: 60S ribosomal protein L7-A
    • Protein or peptide: 60S ribosomal protein L14-A
    • Protein or peptide: 60S ribosomal protein L16-A
    • Protein or peptide: 60S ribosomal protein L18-A
    • Protein or peptide: 60S ribosomal protein L20-A
    • Protein or peptide: 60S ribosomal protein L32
    • Protein or peptide: 60S ribosomal protein L33-A
    • Protein or peptide: Ribosomal RNA-processing protein 1
    • RNA: 25S ribosomal RNA
    • RNA: 5.8S ribosomal RNA
    • Protein or peptide: Nucleolar protein 4

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Supramolecule #1: Yeast pre-60S Domain II

SupramoleculeName: Yeast pre-60S Domain II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Details: Noc2-TAP particle from yeast after Rpl7 depletion, where only Domain II adopts a structured conformation
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Ribosome biogenesis protein MAK21

MacromoleculeName: Ribosome biogenesis protein MAK21 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 116.832359 KDa
SequenceString: MSENNGNPLD LSSLRNKISS KLRDNNSKKA KKTHKGKDVK ASSNSKKVNE DIRREALALG ASEEDLKLIQ GLSDDDDAKS EQEFDAVAD EDADDKGFKN DLQNFMKNVG FDQHKLEDVD DDDIEEESTS SKESKIPAQE KEHAQSNIAS STIEKTSQES I DNGSEQEE ...String:
MSENNGNPLD LSSLRNKISS KLRDNNSKKA KKTHKGKDVK ASSNSKKVNE DIRREALALG ASEEDLKLIQ GLSDDDDAKS EQEFDAVAD EDADDKGFKN DLQNFMKNVG FDQHKLEDVD DDDIEEESTS SKESKIPAQE KEHAQSNIAS STIEKTSQES I DNGSEQEE NTVEEANLSS DQEPESESAE KEKKEEKDGG LITQTTIISS DKLIIPYDKP WYEIPLDPQV GQNDDVEELS KE QIEKLFE RGKQTLEADN QTYYEEFTKD SSQAKFMSQI LSDGTLNDKI SAVTLLIQDS PLHNTKSLET LVSYCGKKSR NSA LQSLNA LKDLFLNGLL PNRKLRYFKN QPGLSMMLNK KTLAIFYFED YLKKLFFRVL EVLEVLSHDP IIHVRLQILN HVFD LLTNQ PEQEFNLLRL GVNKIGDIDS KVSSKASYLL LKLEQAHPNM KSIVIDAIVD IALRPNADYH TTYYSVITLN QTILK RSED SVANKLVKTY FTLFEKFLIN TDKDNTNGVV KSNSKSYEEK RKKNFKKGKH GGKSVKIEKT ENEVLDEKNS KLFSAL LTG INRAFPFAQI PASVYEVHME TLFKITHSSN FNTSIQALVL INQVTVKAKL NSDRYYRTLY ESLFDPRLVN SSKQGIY LN LLYKSLKQDA LNVERVEAFV KRILQVCSHW LNVGTITGFF FLLIQLAKTV PQIKNLLTNT PVDYEYESDA EEEQGDKD I KRKEYDGRKR DPKFANAEKS SLWEINNFIN HFHPTVKTYA NAYVTGETEQ IAKPDLGLFT LSHFLDRFVY RSAKQTNTA RGTSIMQPLF SGSRVNDSVL VKASDIMHDQ GPVNTEDWLT KKVEDIKPED KFFYQYFTTK KTADGKGKKS NKASNFDSDD EMDENEIWS ALVKSRPDVE DDSDDSELDF AEDDFSDSTS DDEPKLDAID DEDAKSEGSQ ESDQEEGLDE DIFYSFDGEQ D NSDKKRSF AESSEEDESS EEEKEEEENK EVSAKRAKKK QRKNMLKSLP VFASADDYAQ YLDQDSD

UniProtKB: Ribosome biogenesis protein MAK21

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Macromolecule #2: Nucleolar complex protein 2

MacromoleculeName: Nucleolar complex protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 81.719289 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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: Nucleolar complex protein 2

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Macromolecule #3: 60S ribosomal protein L4-A

MacromoleculeName: 60S ribosomal protein L4-A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.159125 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSRPQVTVHS LTGEATANAL PLPAVFSAPI RPDIVHTVFT SVNKNKRQAY AVSEKAGHQT SAESWGTGRA VARIPRVGGG GTGRSGQGA FGNMCRGGRM FAPTKTWRKW NVKVNHNEKR YATASAIAAT AVASLVLARG HRVEKIPEIP LVVSTDLESI Q KTKEAVAA ...String:
MSRPQVTVHS LTGEATANAL PLPAVFSAPI RPDIVHTVFT SVNKNKRQAY AVSEKAGHQT SAESWGTGRA VARIPRVGGG GTGRSGQGA FGNMCRGGRM FAPTKTWRKW NVKVNHNEKR YATASAIAAT AVASLVLARG HRVEKIPEIP LVVSTDLESI Q KTKEAVAA LKAVGAHSDL LKVLKSKKLR AGKGKYRNRR WTQRRGPLVV YAEDNGIVKA LRNVPGVETA NVASLNLLQL AP GAHLGRF VIWTEAAFTK LDQVWGSETV ASSKVGYTLP SHIISTSDVT RIINSSEIQS AIRPAGQATQ KRTHVLKKNP LKN KQVLLR LNPYAKVFAA EKLGSKKAEK TGTKPAAVFT ETLKHD

UniProtKB: Large ribosomal subunit protein uL4A

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Macromolecule #4: Protein MAK16

MacromoleculeName: Protein MAK16 / type: protein_or_peptide / ID: 4
Details: ...Details: MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKLYLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMITERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPLNVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLADSDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNAEQEVAQ
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 35.754605 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDEIVWQVI NQSFCSHRIK APNGQNFCRN EYNVTGLCTR QSCPLANSKY ATVKCDNGKL YLYMKTPERA HTPAKLWERI KLSKNYTKA LQQIDEHLLH WSKFFRHKCK QRFTKLTQVM ITERRLALRE EERHYVGVAP KVKRREQNRE RKALVAAKIE K AIEKELMD ...String:
MSDEIVWQVI NQSFCSHRIK APNGQNFCRN EYNVTGLCTR QSCPLANSKY ATVKCDNGKL YLYMKTPERA HTPAKLWERI KLSKNYTKA LQQIDEHLLH WSKFFRHKCK QRFTKLTQVM ITERRLALRE EERHYVGVAP KVKRREQNRE RKALVAAKIE K AIEKELMD RLKSGAYGDK PLNVDEKVWK KIMGQMEEEN SQDEEEDWDE EEESDDGEVE YVADDGEGEY VDVDDLEKWL AD SDREASS ASESESDSES ESDSDSDEEN KNSAKRRKKG TSAKTKRPKV EIEYEEEHEV QNAEQEVAQ

UniProtKB: Protein MAK16

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Macromolecule #5: 60S ribosomal protein L6-A

MacromoleculeName: 60S ribosomal protein L6-A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.000564 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSAQKAPKWY PSEDVAALKK TRKAARPQKL RASLVPGTVL ILLAGRFRGK RVVYLKHLED NTLLISGPFK VNGVPLRRVN ARYVIATST KVSVEGVNVE KFNVEYFAKE KLTKKEKKEA NLFPEQQNKE IKAERVEDQK VVDKALIAEI KKTPLLKQYL S ASFSLKNG DKPHMLKF

UniProtKB: Large ribosomal subunit protein eL6A

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Macromolecule #6: 60S ribosomal protein L7-A

MacromoleculeName: 60S ribosomal protein L7-A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.686281 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAAEKILTPE SQLKKSKAQQ KTAEQVAAER AARKAANKEK RAIILERNAA YQKEYETAER NIIQAKRDAK AAGSYYVEAQ HKLVFVVRI KGINKIPPKP RKVLQLLRLT RINSGTFVKV TKATLELLKL IEPYVAYGYP SYSTIRQLVY KRGFGKINKQ R VPLSDNAI ...String:
MAAEKILTPE SQLKKSKAQQ KTAEQVAAER AARKAANKEK RAIILERNAA YQKEYETAER NIIQAKRDAK AAGSYYVEAQ HKLVFVVRI KGINKIPPKP RKVLQLLRLT RINSGTFVKV TKATLELLKL IEPYVAYGYP SYSTIRQLVY KRGFGKINKQ R VPLSDNAI IEANLGKYGI LSIDDLIHEI ITVGPHFKQA NNFLWPFKLS NPSGGWGVPR KFKHFIQGGS FGNREEFINK LV KSMN

UniProtKB: Large ribosomal subunit protein uL30A

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Macromolecule #7: 60S ribosomal protein L14-A

MacromoleculeName: 60S ribosomal protein L14-A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.195066 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSTDSIVKAS NWRLVEVGRV VLIKKGQSAG KLAAIVEIID QKKVLIDGPK AGVPRQAINL GQVVLTPLTF ALPRGARTAT VSKKWAAAA VCEKWAASSW AKKIAQRERR AALTDFERFQ VMVLRKQKRY TVKKALAKA

UniProtKB: Large ribosomal subunit protein eL14A

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Macromolecule #8: 60S ribosomal protein L16-A

MacromoleculeName: 60S ribosomal protein L16-A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.247227 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSVEPVVVID GKGHLVGRLA SVVAKQLLNG QKIVVVRAEE LNISGEFFRN KLKYHDFLRK ATAFNKTRGP FHFRAPSRIF YKALRGMVS HKTARGKAAL ERLKVFEGIP PPYDKKKRVV VPQALRVLRL KPGRKYTTLG KLSTSVGWKY EDVVAKLEAK R KVSSAEYY ...String:
MSVEPVVVID GKGHLVGRLA SVVAKQLLNG QKIVVVRAEE LNISGEFFRN KLKYHDFLRK ATAFNKTRGP FHFRAPSRIF YKALRGMVS HKTARGKAAL ERLKVFEGIP PPYDKKKRVV VPQALRVLRL KPGRKYTTLG KLSTSVGWKY EDVVAKLEAK R KVSSAEYY AKKRAFTKKV ASANATAAES DVAKQLAALG Y

UniProtKB: Large ribosomal subunit protein uL13A

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Macromolecule #9: 60S ribosomal protein L18-A

MacromoleculeName: 60S ribosomal protein L18-A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.609252 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MGIDHTSKQH KRSGHRTAPK SDNVYLKLLV KLYTFLARRT DAPFNKVVLK ALFLSKINRP PVSVSRIARA LKQEGAANKT VVVVGTVTD DARIFEFPKT TVAALRFTAG ARAKIVKAGG ECITLDQLAV RAPKGQNTLI LRGPRNSREA VRHFGMGPHK G KAPRILST GRKFERARGR RRSKGFKV

UniProtKB: Large ribosomal subunit protein eL18A

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Macromolecule #10: 60S ribosomal protein L20-A

MacromoleculeName: 60S ribosomal protein L20-A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.478852 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MAHFKEYQVI GRRLPTESVP EPKLFRMRIF ASNEVIAKSR YWYFLQKLHK VKKASGEIVS INQINEAHPT KVKNFGVWVR YDSRSGTHN MYKEIRDVSR VAAVETLYQD MAARHRARFR SIHILKVAEI EKTADVKRQY VKQFLTKDLK FPLPHRVQKS T KTFSYKRP STFY

UniProtKB: Large ribosomal subunit protein eL20A

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Macromolecule #11: 60S ribosomal protein L32

MacromoleculeName: 60S ribosomal protein L32 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.809441 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MASLPHPKIV KKHTKKFKRH HSDRYHRVAE NWRKQKGIDS VVRRRFRGNI SQPKIGYGSN KKTKFLSPSG HKTFLVANVK DLETLTMHT KTYAAEIAHN ISAKNRVVIL ARAKALGIKV TNPKGRLALE A

UniProtKB: Large ribosomal subunit protein eL32

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Macromolecule #12: 60S ribosomal protein L33-A

MacromoleculeName: 60S ribosomal protein L33-A / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.17713 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MAESHRLYVK GKHLSYQRSK RVNNPNVSLI KIEGVATPQD AQFYLGKRIA YVYRASKEVR GSKIRVMWGK VTRTHGNSGV VRATFRNNL PAKTFGASVR IFLYPSNI

UniProtKB: Large ribosomal subunit protein eL33A

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Macromolecule #13: Ribosomal RNA-processing protein 1

MacromoleculeName: Ribosomal RNA-processing protein 1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 33.250531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: METSNFVKQL SSNNRKTRVN ALEALKKYLT AKQFKENKQI EFNKLWKGLY YAMWFSDRPR PQQRLANELG ELHGLYFDPK DNSTADELT TNDKAFIKFS RGFWKVMCFE WFNIDRYRLD KYLLLIRRVL FSQLKYLQSR NWDKKLVDEY IKKVLRWLPL S GSPKVYTG ...String:
METSNFVKQL SSNNRKTRVN ALEALKKYLT AKQFKENKQI EFNKLWKGLY YAMWFSDRPR PQQRLANELG ELHGLYFDPK DNSTADELT TNDKAFIKFS RGFWKVMCFE WFNIDRYRLD KYLLLIRRVL FSQLKYLQSR NWDKKLVDEY IKKVLRWLPL S GSPKVYTG IPIHIVDILL DEWERLLKDG DEDDEDEENK EEEMRKIAES AKKTPLADVI AIFQDIVADY NNSKVLREKI KE DLFSDTR LVSWDILEGE TQHNDSSNES EEEEEEEWKG F

UniProtKB: Ribosomal RNA-processing protein 1

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Macromolecule #16: Nucleolar protein 4

MacromoleculeName: Nucleolar protein 4 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 77.97243 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEETIENVEV PSSNVSKQND DGLDMKTLFV RSIPQDVTDE QLADFFSNFA PIKHAVVVKD TNKRSRGFGF VSFAVEDDTK EALAKARKT KFNGHILRVD IAKRRDRSKK TSEVVEKSTP ESSEKITGQN NEDEDDADGE DSMLKGKPKL IIRNMPWSCR D PVKLKKIF ...String:
MEETIENVEV PSSNVSKQND DGLDMKTLFV RSIPQDVTDE QLADFFSNFA PIKHAVVVKD TNKRSRGFGF VSFAVEDDTK EALAKARKT KFNGHILRVD IAKRRDRSKK TSEVVEKSTP ESSEKITGQN NEDEDDADGE DSMLKGKPKL IIRNMPWSCR D PVKLKKIF GRYGTVVEAT IPRKRDGKLC GFAFVTMKKI SNCRIALENT KDLKIDGRKV AVDFAVQKNR WEDYKKAQPE MN DKDDNES GNEDAEENHD DEEDENEEED RQVDQASKNK ESKRKAQNKR EDFSVFVRNV PYDATEESLA PHFSKFGSVK YAL PVIDKS TGLAKGTAFV AFKDQYTYNE CIKNAPAAGS TSLLIGDDVM PEYVYEGRVL SITPTLVRED AGRMAEKNAA KRKE ALGKA PGEKDRRNLY LLNEGRVVEG SKMADLLTNT DMEIREKSYK LRVEQLKKNP SLHLSMTRLA IRNLPRAMND KALKA LARK AVVEFATEVK NKERHPLSKE EIIRSTKEKY KFMGPDEIEA QKKKDKKSGV VKQAKVIMEV KGSTAGRSRG YGFVEF RDH KNALMGLRWL NCHAVTSDEI LEGLNDDEKK QVDNDLGKGR RLCVEFAIEN SNVVKRRREQ LKQARTKRTR PDNEDTG DV GESENKKPKK EEATTPTNPD DKKMGDDIKR IIGFKRKRKH AKK

UniProtKB: Nucleolar protein 4

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Macromolecule #14: 25S ribosomal RNA

MacromoleculeName: 25S ribosomal RNA / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.0974938749999998 MDa
SequenceString: GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAA CGGCGAGUGA AGCGGCAAAA GCUCAAAUUU GAAAUCUGGU ACCUUCGGUG CCCGAGUUGU AAUUUGGAGA G GGCAACUU ...String:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAA CGGCGAGUGA AGCGGCAAAA GCUCAAAUUU GAAAUCUGGU ACCUUCGGUG CCCGAGUUGU AAUUUGGAGA G GGCAACUU UGGGGCCGUU CCUUGUCUAU GUUCCUUGGA ACAGGACGUC AUAGAGGGUG AGAAUCCCGU GUGGCGAGGA GU GCGGUUC UUUGUAAAGU GCCUUCGAAG AGUCGAGUUG UUUGGGAAUG CAGCUCUAAG UGGGUGGUAA AUUCCAUCUA AAG CUAAAU AUUGGCGAGA GACCGAUAGC GAACAAGUAC AGUGAUGGAA AGAUGAAAAG AACUUUGAAA AGAGAGUGAA AAAG UACGU GAAAUUGUUG AAAGGGAAGG GCAUUUGAUC AGACAUGGUG UUUUGUGCCC UCUGCUCCUU GUGGGUAGGG GAAUC UCGC AUUUCACUGG GCCAGCAUCA GUUUUGGUGG CAGGAUAAAU CCAUAGGAAU GUAGCUUGCC UCGGUAAGUA UUAUAG CCU GUGGGAAUAC UGCCAGCUGG GACUGAGGAC UGCGACGUAA GUCAAGGAUG CUGGCAUAAU GGUUAUAUGC CGCCCGU CU UGAAACACGG ACCAAGGAGU CUAACGUCUA UGCGAGUGUU UGGGUGUAAA ACCCAUACGC GUAAUGAAAG UGAACGUA G GUUGGGGCCU CGCAAGAGGU GCACAAUCGA CCGAUCCUGA UGUCUUCGGA UGGAUUUGAG UAAGAGCAUA GCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAU CGUCGAAUUU GGGUAUAGGG GCGAAAGACU AAUCGAACCA UCUAGUAGCU GGUUCCUGCC GAAGUUUCCC U CAGGAUAG CAGAAGCUCG UAUCAGUUUU AUGAGGUAAA GCGAAUGAUU AGAGGUUCCG GGGUCGAAAU GACCUUGACC UA UUCUCAA ACUUUAAAUA UGUAAGAAGU CCUUGUUACU UAAUUGAACG UGGACAUUUG AAUGAAGAGC UUUUAGUGGG CCA UUUUUG GUAAGCAGAA CUGGCGAUGC GGGAUGAACC GAACGUAGAG UUAAGGUGCC GGAAUACACG CUCAUCAGAC ACCA CAAAA GGUGUUAGUU CAUCUAGACA GCCGGACGGU GGCCAUGGAA GUCGGAAUCC GCUAAGGAGU GUGUAACAAC UCACC GGCC GAAUGAACUA GCCCUGAAAA UGGAUGGCGC UCAAGCGUGU UACCUAUACU CUACCGUCAG GGUUGAUAUG AUGCCC UGA CGAGUAGGCA GGCGUGGAGG UCAGUGACGA AGCCUAGACC GUAAGGUCGG GUCGAACGGC CUCUAGUGCA GAUCUUG GU GGUAGUAGCA AAUAUUCAAA UGAGAACUUU GAAGACUGAA GUGGGGAAAG GUUCCACGUC AACAGCAGUU GGACGUGG G UUAGUCGAUC CUAAGAGAUG GGGAAGCUCC GUUUCAAAGG CCUGAUUUUA UGCAGGCCAC CAUCGAAAGG GAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUU CUUCUUAACA GCUUAUCACC CCGGAAUUGG UUUAUCCGGA GAUGGGGUCU UAUGGCUGGA AGAGGCCAGC A CCUUUGCU GGCUCCGGUG CGCUUGUGAC GGCCCGUGAA AAUCCACAGG AAGGAAUAGU UUUCAUGCCA GGUCGUACUG AU AACCGCA GCAGGUCUCC AAGGUGAACA GCCUCUAGUU GAUAGAAUAA UGUAGAUAAG GGAAGUCGGC AAAAUAGAUC CGU AACUUC GGGAUAAGGA UUGGCUCUAA GGGUCGGGUA GUGAGGGCCU UGGUCAGACG CAGCGGGCGU GCUUGUGGAC UGCU UGGUG GGGCUUGCUC UGCUAGGCGG ACUACUUGCG UGCCUUGUUG UAGACGGCCU UGGUAGGUCU CUUGUAGACC GUCGC UUGC UACAAUUAAC GAUCAACUUA GAACUGGUAC GGACAAGGGG AAUCUGACUG UCUAAUUAAA ACAUAGCAUU GCGAUG GUC AGAAAGUGAU GUUGACGCAA UGUGAUUUCU GCCCAGUGCU CUGAAUGUCA AAGUGAAGAA AUUCAACCAA GCGCGGG UA AACGGCGGGA GUAACUAUGA CUCUCUUAAG GUAGCCAAAU GCCUCGUCAU CUAAUUAGUG ACGCGCAUGA AUGGAUUA A CGAGAUUCCC ACUGUCCCUA UCUACUAUCU AGCGAAACCA CAGCCAAGGG AACGGGCUUG GCAGAAUCAG CGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUAC CACUACCUUU AUAGUUUCUU UACUUAUUCA AUGAAGCGGA GCUGGAAUUC AUUUUCCACG UUCUAGCAUU C AAGGUCCC AUUCGGGGCU GAUCCGGGUU GAAGACAUUG UCAGGUGGGG AGUUUGGCUG GGGCGGCACA UCUGUUAAAC GA UAACGCA GAUGUCCUAA GGGGGGCUCA UGGAGAACAG AAAUCUCCAG UAGAACAAAA GGGUAAAAGC CCCCUUGAUU UUG AUUUUC AGUGUGAAUA CAAACCAUGA AAGUGUGGCC UAUCGAUCCU UUAGUCCCUC GGAAUUUGAG GCUAGAGGUG CCAG AAAAG UUACCACAGG GAUAACUGGC UUGUGGCAGU CAAGCGUUCA UAGCGACAUU GCUUUUUGAU UCUUCGAUGU CGGCU CUUC CUAUCAUACC GAAGCAGAAU UCGGUAAGCG UUGGAUUGUU CACCCACUAA UAGGGAACGU GAGCUGGGUU UAGACC GUC GUGAGACAGG UUAGUUUUAC CCUACUGAUG AAUGUUACCG CAAUAGUAAU UGAACUUAGU ACGAGAGGAA CAGUUCA UU CGGAUAAUUG GUUUUUGCGG CUGUCUGAUC AGGCAUUGCC GCGAAGCUAC CAUCCGCUGG AUUAUGGCUG AACGCCUC U AAGUCAGAAU CCAUGCUAGA ACGCGGUGAU UUCUUUGCUC CACACAAUAU AGAUGGAUAC GAAUAAGGCG UCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGG GGAUAAAUCA UUUGUAUACG ACUUAGAUGU ACAACGGGGU AUUGUAAGCA GUAGAGUAGC CUUGUUGUUA C GAUCUGCU GAGAUUAAGC CUUUGUUGUC UGAUUUGU

GENBANK: GENBANK: CP011821.1

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Macromolecule #15: 5.8S ribosomal RNA

MacromoleculeName: 5.8S ribosomal RNA / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 51.012129 KDa
SequenceString:
AAAACUUUCA ACAACGGAUC UCUUGGUUCU CGCAUCGAUG AAGAACGCAG CGAAAUGCGA UACGUAAUGU GAAUUGCAGA AUUCCGUGA AUCAUCGAAU CUUUGAACGC ACAUUGCGCC CCUUGGUAUU CCAGGGGGCA UGCCUGUUUG AGCGUCAUUU

GENBANK: GENBANK: MK267784.1

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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: 7.5
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 4 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11250 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.0 - 4.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0 - 4.6) / Number images used: 54106
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.0 - 4.6)
FSC plot (resolution estimation)

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