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Basic information

Entry
Database: EMDB / ID: EMD-75578
TitleYeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP* - Composite map
Map data
Sample
  • Complex: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
    • RNA: 25S ribosomal RNA
    • Protein or peptide: 60S ribosomal protein L8-A
    • Protein or peptide: 60S ribosomal protein L15-A
    • Protein or peptide: Periodic tryptophan protein 1
    • Protein or peptide: Ribosome biogenesis protein BRX1
    • Protein or peptide: 60S ribosomal protein L36-A
    • Protein or peptide: rRNA-processing protein EBP2
  • Ligand: MAGNESIUM ION
Keywordsribosome biogenesis / co-transcriptional assembly / RNA-binding protein / nucleolar RNP / RIBOSOME
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPiwowarczyk R / Klinge S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM145950-03 United States
Chan Zuckerberg Initiative2023-332391 United States
CitationJournal: Biorxiv / Year: 2026
Title: Mechanism for the initiation of co-transcriptional pre-60 S assembly.
Authors: Piwowarczyk R / Klinge S
History
DepositionFeb 13, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75578.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 1.0626 Å
Density
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-38.649386999999997 - 69.786910000000006
Average (Standard dev.)0.002437314 (±1.044784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.78 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP

EntireName: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
Components
  • Complex: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
    • RNA: 25S ribosomal RNA
    • Protein or peptide: 60S ribosomal protein L8-A
    • Protein or peptide: 60S ribosomal protein L15-A
    • Protein or peptide: Periodic tryptophan protein 1
    • Protein or peptide: Ribosome biogenesis protein BRX1
    • Protein or peptide: 60S ribosomal protein L36-A
    • Protein or peptide: rRNA-processing protein EBP2
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP

SupramoleculeName: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: 25S ribosomal RNA

MacromoleculeName: 25S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288C (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: NR_132207.1

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Macromolecule #2: 60S ribosomal protein L8-A

MacromoleculeName: 60S ribosomal protein L8-A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
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: Large ribosomal subunit protein eL8A

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Macromolecule #3: 60S ribosomal protein L15-A

MacromoleculeName: 60S ribosomal protein L15-A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
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

UniProtKB: Large ribosomal subunit protein eL15A

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Macromolecule #4: Periodic tryptophan protein 1

MacromoleculeName: Periodic tryptophan protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 63.872137 KDa
SequenceString: MISATNWVPR GFSSEFPEKY VLDDEEVERI NQLAQLNLDD AKATLEEAEG ESGVEDDAAT GSSNKLKDQL DIDDDLKEYN LEEYDDEEI ADNEGGKDVS MFPGLSNDSD VKFHEGEKGE DPYISLPNQE DSQEEKQELQ VYPSDNLVLA ARTEDDVSYL D IYVYDDGA ...String:
MISATNWVPR GFSSEFPEKY VLDDEEVERI NQLAQLNLDD AKATLEEAEG ESGVEDDAAT GSSNKLKDQL DIDDDLKEYN LEEYDDEEI ADNEGGKDVS MFPGLSNDSD VKFHEGEKGE DPYISLPNQE DSQEEKQELQ VYPSDNLVLA ARTEDDVSYL D IYVYDDGA GFHSSDIPVE EGDEADPDVA RGLVRDPALY VHHDLMLPAF PLCVEWLDYK VGSNSEEAAN YAAIGTFDPQ IE IWNLDCV DKAFPDMILG EPLDNSMVSL KSKKKKKKSK TGHITTHHTD AVLSMAHNKY FRSVLASTSA DHTVKLWDLN SGN AARSLA SIHSNKNVSS SEWHMLNGSI LLTGGYDSRV ALTDVRISDE SQMSKYWSAM AGEEIETVTF ASENIILCGT DSGN VYSFD IRNNENRKPV WTLKAHDAGI STLCSNKFIP GMMSTGAMGE KTVKLWKFPL DDATNTKGPS MVLSRDFDVG NVLTS SFAP DIEVAGTMVI GGVNKVLKLW DVFTNRSVRK SFKSELENVQ ARAKEEAQKI GKSSRIARKY TSNDNPDTVI TIDDQG EDE EEREGGDEHD DMA

UniProtKB: Periodic tryptophan protein 1

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Macromolecule #5: Ribosome biogenesis protein BRX1

MacromoleculeName: Ribosome biogenesis protein BRX1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 33.585414 KDa
SequenceString: MSSIYKALAG KSKDNKSEKK QGNVKQFMNK QRTLLISSRG VNYRHRHLIQ DLSGLLPHSR KEPKLDTKKD LQQLNEIAEL YNCNNVLFF EARKHQDLYL WLSKPPNGPT IKFYIQNLHT MDELNFTGNC LKGSRPVLSF DQRFESSPHY QLIKELLVHN F GVPPNARK ...String:
MSSIYKALAG KSKDNKSEKK QGNVKQFMNK QRTLLISSRG VNYRHRHLIQ DLSGLLPHSR KEPKLDTKKD LQQLNEIAEL YNCNNVLFF EARKHQDLYL WLSKPPNGPT IKFYIQNLHT MDELNFTGNC LKGSRPVLSF DQRFESSPHY QLIKELLVHN F GVPPNARK SKPFIDHVMS FSIVDDKIWV RTYEISHSTK NKEEYEDGEE DISLVEIGPR FVMTVILILE GSFGGPKIYE NK QYVSPNV VRAQIKQQAA EEAKSRAEAA VERKIKRREN VLAADPLSND ALFK

UniProtKB: Ribosome biogenesis protein BRX1

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Macromolecule #6: 60S ribosomal protein L36-A

MacromoleculeName: 60S ribosomal protein L36-A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 11.151259 KDa
SequenceString:
MTVKTGIAIG LNKGKKVTSM TPAPKISYKK GAASNRTKFV RSLVREIAGL SPYERRLIDL IRNSGEKRAR KVAKKRLGSF TRAKAKVEE MNNIIAASRR H

UniProtKB: Large ribosomal subunit protein eL36A

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Macromolecule #7: rRNA-processing protein EBP2

MacromoleculeName: rRNA-processing protein EBP2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 49.842613 KDa
SequenceString: MAKGFKLKEL LSHQKEIEKA EKLENDLKKK KSQELKKEEP TIVTASNLKK LEKKEKKADV KKEVAADTEE YQSQALSKKE KRKLKKELK KMQEQDATEA QKHMSGDEDE SGDDREEEEE EEEEEEGRLD LEKLAKSDSE SEDDSESEND SEEDEDVVAK E ESEEKEEQ ...String:
MAKGFKLKEL LSHQKEIEKA EKLENDLKKK KSQELKKEEP TIVTASNLKK LEKKEKKADV KKEVAADTEE YQSQALSKKE KRKLKKELK KMQEQDATEA QKHMSGDEDE SGDDREEEEE EEEEEEGRLD LEKLAKSDSE SEDDSESEND SEEDEDVVAK E ESEEKEEQ EEEQDVPLSD VEFDSDADVV PHHKLTVNNT KAMKHALERV QLPWKKHSFQ EHQSVTSETN TDEHIKDIYD DT ERELAFY KQSLDAVLVA RDELKRLKVP FKRPLDYFAE MVKSDEHMDK IKGKLIEEAS DKKAREEARR QRQLKKFGKQ VQN ATLQKR QLEKRETLEK IKSLKNKRKH NEIDHSEFNV GVEEEVEGKR FDRGRPNGKR AAKNAKYGQG GMKRFKRKND ATSS ADVSG FSSRKMKGKT NRPGKSRRAR RF

UniProtKB: rRNA-processing protein EBP2

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R3.5/1 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 242741
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

8e5t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-10zz:
Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP*

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