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- PDB-6nd4: Conformational switches control early maturation of the eukaryoti... -

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Basic information

Entry
Database: PDB / ID: 6nd4
TitleConformational switches control early maturation of the eukaryotic small ribosomal subunit
Components
  • 18S rRNA 5' domain start
  • 5'ETS rRNA
  • Bud21
  • Imp3
  • Mpp10
  • Nop1.1
  • Nop56
  • Nop58
  • Rrp9
  • Snu13NHP2L1
  • Sof1
  • U3 snoRNA
  • Unidentified fragment
  • Utp1
  • Utp10
  • Utp12
  • Utp13
  • Utp15
  • Utp17
  • Utp18
  • Utp21
  • Utp24
  • Utp4
  • Utp5
  • Utp6
  • Utp7
  • Utp8
  • Utp9
KeywordsRIBOSOME / Ribosome assembly
Function / homology
Function and homology information


t-UTP complex / RNA fragment catabolic process / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis ...t-UTP complex / RNA fragment catabolic process / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis / snRNA binding / positive regulation of RNA binding / SUMOylation of RNA binding proteins / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / rRNA methyltransferase activity / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / U4 snRNP / rRNA methylation / U3 snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / snoRNA binding / spliceosomal complex assembly / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / spliceosomal complex / ribosomal small subunit biogenesis / mRNA splicing, via spliceosome / ribosomal small subunit assembly / rRNA processing / small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
U3 small nucleolar RNA-associated protein 8 / Utp8 family / U3 snoRNA associated / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1, PIN domain / U3 small nucleolar RNA-associated protein 6 / Sof1-like protein / BING4, C-terminal domain / Ribosomal RNA-processing protein Rrp9-like ...U3 small nucleolar RNA-associated protein 8 / Utp8 family / U3 snoRNA associated / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1, PIN domain / U3 small nucleolar RNA-associated protein 6 / Sof1-like protein / BING4, C-terminal domain / Ribosomal RNA-processing protein Rrp9-like / WD repeat-containing protein WDR46/Utp7 / Sof1-like domain / BING4CT (NUC141) domain / BING4CT (NUC141) domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / BP28, C-terminal domain / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Utp21 specific WD40 associated putative domain / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Large family of predicted nucleotide-binding domains / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / PIN domain / HEAT repeat profile. / HEAT, type 2 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / PIN-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / 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 / Armadillo-like helical / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / rRNA 2'-O-methyltransferase fibrillarin / Periodic tryptophan protein 2 / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 ...RNA / RNA (> 10) / RNA (> 100) / rRNA 2'-O-methyltransferase fibrillarin / Periodic tryptophan protein 2 / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein SOF1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 6 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 5 / U3 small nucleolar RNA-associated protein 15 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA-processing protein 9 / U3 small nucleolar RNA-associated protein 4 / U3 small nucleolar RNA-associated protein 16 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsHunziker, M. / Barandun, J. / Klinge, S.
Funding support United States, Switzerland, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
CitationJournal: Elife / Year: 2019
Title: Conformational switches control early maturation of the eukaryotic small ribosomal subunit.
Authors: Mirjam Hunziker / Jonas Barandun / Olga Buzovetsky / Caitlin Steckler / Henrik Molina / Sebastian Klinge /
Abstract: Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent ...Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent from the mature ribosome. The subsequent co-transcriptional association of ribosome assembly factors with pre-ribosomal RNA results in the formation of the small subunit processome. Here we show that stable rRNA domains of the small ribosomal subunit can independently recruit their own biogenesis factors in vivo. The final assembly and compaction of the small subunit processome requires the presence of the 5' external transcribed spacer RNA and all ribosomal RNA domains. Additionally, our cryo-electron microscopy structure of the earliest nucleolar pre-ribosomal assembly - the 5' external transcribed spacer ribonucleoprotein - provides a mechanism for how conformational changes in multi-protein complexes can be employed to regulate the accessibility of binding sites and therefore define the chronology of maturation events during early stages of ribosome assembly.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Structure summary / Category: entity / pdbx_entry_details
Item: _entity.pdbx_description / _pdbx_entry_details.sequence_details
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 18, 2019Group: Other / Polymer sequence / Category: atom_sites / entity_poly
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _entity_poly.pdbx_seq_one_letter_code
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
0: 5'ETS rRNA
1: 18S rRNA 5' domain start
2: U3 snoRNA
H: Utp17
I: Utp8
J: Utp15
K: Utp9
L: Utp5
M: Utp10
N: Utp4
O: Utp1
P: Utp6
Q: Utp12
R: Utp13
S: Utp18
T: Utp21
U: Sof1
W: Utp7
Z: Imp3
A: Mpp10
D: Bud21
a: Nop56
b: Nop58
c: Nop1.1
d: Nop1.1
e: Snu13
f: Snu13
g: Rrp9
l: Utp24
x: Unidentified fragment


Theoretical massNumber of molelcules
Total (without water)1,867,66330
Polymers1,867,66330
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, microscopy, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 012

#1: RNA chain 5'ETS rRNA


Mass: 220317.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#2: RNA chain 18S rRNA 5' domain start


Mass: 3727.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
#3: RNA chain U3 snoRNA


Mass: 46932.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)

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Protein , 24 types, 26 molecules HIJKLMNOPQRSTUWZADabcdefgl

#4: Protein Utp17


Mass: 96363.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q02931*PLUS
#5: Protein Utp8


Mass: 49062.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P53276*PLUS
#6: Protein Utp15 / / U3 snoRNA-associated protein 15 / U three protein 15 / U3 protein 15 required for transcription / t-UTP15


Mass: 57765.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q04305
#7: Protein Utp9


Mass: 19935.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P38882*PLUS
#8: Protein Utp5 / U3 snoRNA-associated protein 5 / U three protein 5 / U3 protein 5 required for transcription / t-UTP5


Mass: 72079.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q04177
#9: Protein Utp10 / U3 snoRNA-associated protein 10 / U three protein 10 / U3 protein 10 required for transcription / t-UTP10


Mass: 200298.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P42945
#10: Protein Utp4 /


Mass: 81782.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q06679*PLUS
#11: Protein Utp1 / U three protein 1 / U3 small nucleolar RNA-associated protein 1 / U3 snoRNA-associated protein 1


Mass: 104097.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P25635
#12: Protein Utp6 /


Mass: 46820.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q02354*PLUS
#13: Protein Utp12


Mass: 102690.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q12220*PLUS
#14: Protein Utp13


Mass: 68142.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q05946*PLUS
#15: Protein Utp18 / / U3 snoRNA-associated protein 18 / U three protein 18


Mass: 66494.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P40362
#16: Protein Utp21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q06078
#17: Protein Sof1 / U3 small nucleolar RNA-associated protein SOF1 / U3 snoRNA-associated protein SOF1


Mass: 56888.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P33750
#18: Protein Utp7 / U3 snoRNA-associated protein 7 / U three protein 7


Mass: 62418.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P40055
#19: Protein Imp3 / / U3 snoRNP protein IMP3 / Interacting with MPP10 protein 3


Mass: 21928.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P32899
#20: Protein Mpp10 / U3 snoRNA-associated protein MPP10 / M phase phosphoprotein 10


Mass: 67042.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P47083
#21: Protein Bud21 / U three protein 16 / U3 small nucleolar RNA-associated protein 16 / U3 snoRNA-associated protein 16


Mass: 24431.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q08492
#22: Protein Nop56


Mass: 55307.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q12460*PLUS
#23: Protein Nop58 /


Mass: 53133.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q12499*PLUS
#24: Protein Nop1.1 / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1


Mass: 34525.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#25: Protein Snu13 / NHP2L1 / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13582.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: P39990
#26: Protein Rrp9 /


Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q06506
#27: Protein Utp24 / FAF1-copurifying factor 1


Mass: 21650.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q05498

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Protein/peptide , 1 types, 1 molecules x

#28: Protein/peptide Unidentified fragment


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast)

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Details

Sequence detailsThe complete sample sequence of 5'ETS rRNA is AUGCGAAAGCAGUUGAAGACAAGUUCGAAAAGAGUUUGGAAACGAAUUCG ...The complete sample sequence of 5'ETS rRNA is AUGCGAAAGCAGUUGAAGACAAGUUCGAAAAGAGUUUGGAAACGAAUUCG AGUAGGCUUGUCGUUCGUUAUGUUUUUGUAAAUGGCCUCGUCAAACGGUG GAGAGAGUCGCUAGGUGAUCGUCAGAUCUGCCUAGUCUCUAUACAGCGUG UUUAAUUGACAUGGGUUGAUGCGUAUUGAGAGAUACAAUUUGGGAAGAAA UUCCCAGAGUGUGUUUCUUUUGCGUUUAACCUGAACAGUCUCAUCGUGGG CAUCUUGCGAUUCCAUUGGUGAGCAGCGAAGGAUUUGGUGGAUUACUAGC UAAUAGCAAUCUAUUUCAAAGAAUUCAAACUUGGGGGAAUGCCUUGUUGA AUAGCCGGUCGCAAGACUGUGAUUCUUCAAGUGUAACCUCCUCUCAAAUC AGCGAUAUCAAACGUACCAUUCCGUGAAACACCGGGGUAUCUGUUUGGUG GAACCUGAUUAGAGGAAACUCAAAGAGUGCUAUGGUAUGGUGACGGAGUG CGCUGGUCAAGAGUGUAAAAGCUUUUUGAACAGAGAGCAUUUCCGGCAGC AGAGAGACCUGAAAAAGCAAUUUUUCUGGAAUUUCAGCUGUUUCCAAACU CAAUAAGUAUCUUCUAGCAAGAGGGAAUAGGUGGGAAAAAAAAAAAGAGA UUUCGGUUUCUUUCUUUUUUACUGCUUGUUGCUUCUUCUUUUAAGAUAGU The complete sample sequence of Utp 17 is MTQSLGIEQYKLSVVSGGKPALNNLSSVTGNKNIARLSQDQRNYIIPFNNQIKVYSVET RQCVKTLKFANNSLLSGIFLQEEENNESIVKILLGDITVPQQEDAHLITVFTNNGHVIV LNYKGKLVESPKHFKISLADEKLANVFHSEGNYRILTTFKDPSQKAHNSLQSYRLYALT FDDAKKQFEVAHQAEWHNVILSNISSNGKLLAHMCKDVSTKDHEHKSISVVSLFDDSVN LSFPLGSILSSQTQSLSYNTRYVSSMAIDNMGQQLAVGFASGVISIVSLADLQIRLLKW HIDSVLSLSFSHDGSYLLSGGWEKVMSLWQLETNSQQFLPRLNGIIIDCQVLGPQGNYY SLILQMTENNSNSDYQFLLLNASDLTSKLSINGPLPVFNSTIKHIQQPISAMNTKNSNS ITSLNHSKKKQSRKLIKSRRQDFTTNVEINPINKNLYFPHISAVQIFDFYKNEQVNYQY LTSGVNNSMGKVRFELNLQDPIITDLKFTKDGQWMITYEIEYPPNDLLSSKDLTHILKF WTKNDNETNWNLKTKVINPHGISVPITKILPSPRSVNNSQGCLTADNNGGLKFWSFDSH ESNWCLKKISLPNFNHFSNSVSLAWSQDGSLIFHGFDDKLQILDFDTFKKFESLENTKT VSEFTLDSEIQTVKLINDTNLIVATRTTLNAINLLRGQVINSFDLYPFVNGVYKNGHMD RLITCDERTGNIALVINQQLTDLDGVPTINYKSRIIIFDSDLSTKLGNFTHHEYISWIG WNYDTDFIFLDIESTLGVVGTTVNTQLSDEVNNEGILDGLVSNTITTSASNSDIFAEQL HKLSSRGKKSDTRDKNTNDNDEDEEDIALEFINGEKKDKLVNMNSFTSMFDNIQNVQMD TFFDRVMKVLT The complete sample sequence of Utp8 is MPSLSQPFRLATLPKIASLSNFSLQADYVQVADGTFNESTNNITLGISGSSISQYIINPT PKLTFDYPIPSTNIITACNAEKGQANIDGNIEASTDDEANNEKTINTQKKRNVEIWAFGL MVNKGNYTLNVITKALEDTTDTSNDHLSESDIDNKAYTGSDEFLSQYKIKAKAKVMSIKI DTKNSLVIAILQNGLIEIFDFKLTLLHSFDISYDNLKYAKWFTENGTEYVFVLCPLQDDK VCYKLLELTDCGSGESSPIKELSSTIIEGFSFENSKLCYQFGKLYKLNQGKIYIYSLPHC QLQQVIEFPMVDKLSPGDDLISFQPVSVNRVLLTVNNVIYLLDLLHCSTLSQRELTHVKT FQLLKSAVINSEKSHNSKTIAIGISTKNGPNPTSSLEIINIDVGTNTLKDSLGKSFQVGN NDSSVILKPLFDDKDINDKRVKCNDVSGDSSVPVLHCNEVIEKLSALQDNDITSFDDIFF KELKIKEEHYTEKDRYISDPGFLNKVLDLIFGKFSGNDYPKTLTFLLTHPLFPLSRTRNL LSLLRDQPRLFKQAIVTCPNLPLNELLEELFSIRNRELLLDISFRILQDFTRDSIKQEMK KLSKLDVQNFIEFITSGGEDSSPECFNPSQSTQLFQLLSLVLDSIGLFSLEGALLENLTL YIDKQVEIAERNTELWNLIDTKGFQHGFASSTFDNGTSQKRALPTYTMEYLDI The complete sample sequence of Utp9 is MGSSLDLVASFSHDSTRFAFQASVAQKNNVDIYPLNETKDYVVNSSLVSHIDYETNDMKV SDVIFFGWCSDLIDTQSSNIKRKLDEDEGTGESSEQRCENFFVNGFPDGRIVVYSSNGKD IVNIIKNKKEILGADTDESDIWILDSDKVVKKLQYNNSKPLKTFTLVDGKDDEIVHFQIL HQNGTLLVCIITKQMVYIVDPSKRRPSTKYSFEISDAVACEFSSDGKYLLIANNEELIAY DLKEDSKLIQSWPVQVKTLKTLDDLIMALTTDGKINNYKIGEADKVCSIVVNEDLEIIDF TPINSKQQVLISWLNVNEPNFESISLKEIETQGYITINKNEKNNADEADQKKLEEKEEEA QPEVQHEKKETETKINKKVSKSDQVEIANILSSHLEANSTEILDDLMSGSWTEPEIKKFI LTKINTVDHLSKIFLTISKSITQNPWNEENLLPLWLKWLLTLKSGELNSIKDKHTKKNCK HLKSALRSSEEILPVLLGIQGRLEMLRRQAKLREDLAQLSMQEGEDDEIEVIEHSNVISN PLQDQASPVEKLEPDSIVYANGESDEFVDASEYKD The complete sequence of Utp4 is MSSSLLSVLKEKSRSLKIRNKPVKMTSQERMIVHRCRFVDFTPATITSLAFSHKSNINKL TPSDLRLAIGRSNGNIEIWNPRNNWFQEMVIEGGKDRSIEGLCWSNVNGESLRLFSIGGS TVVTEWDLATGLPLRNYDCNSGVIWSISINDSQDKLSVGCDNGTVVLIDISGGPGVLEHD TILMRQEARVLTLAWKKDDFVIGGCSDGRIRIWSAQKNDENMGRLLHTMKVDKAKKESTL VWSVIYLPRTDQIASGDSTGSIKFWDFQFATLNQSFKAHDADVLCLTTDTDNNYVFSAGV DRKIFQFSQNTNKSQKNNRWVNSSNRLLHGNDIRAICAYQSKGADFLVSGGVEKTLVINS LTSFSNGNYRKMPTVEPYSKNVLVNKEQRLVVSWSESTVKIWTMGTDSSTEQNYKLVCKL TLKDDQNISTCSLSPDGQVLVVGRPSTTKVFHLQPVGNKLKVTKLDNDLLLRTSTKLVKF IDNSKIVICSCEDDVFIVDLESEEDEKPQEVELLEVTSTKSSIKVPYINRINHLEVDQNI AVISRGCGVVDILDLKARISKPLARLNNFITAVHINTSRKSVVVITADNKIYEFNMNLNS EAENEDSESVLTQWSKNNTDNLPKEWKTLKENCVGIFSDIENSSRLWFWGATWISRIDFD VDFPINKRRKQKKRTHEGLTITDESNFMNDEEDDEDDDIDMEISENLNVLLNQGNKIKST DVQRNEESSGHFFFTDKYKPLLFVDLISSNELAIIERNPLTFHSKQKAFIQPKLVF The complete sequence of Utp6 is MSKTRYYLEQCIPEMDDLVEKGLFTKNEVSLIMKKRTDFEHRLNSRGSSINDYIKYINYE SNVNKLRAKRCKRILQVKKTNSLSDWSIQQRIGFIYQRGTNKFPQDLKFWAMYLNYMKAR GNQTSYKKIHNIYNQLLKLHPTNVDIWISCAKYEYEVHANFKSCRNIFQNGLRFNPDVPK LWYEYVKFELNFITKLINRRKVMGLINEREQELDMQNEQKNNQAPDEEKSHLQVPSTGDS MKDKLNELPEADISVLGNAETNPALRGDIALTIFDVCMKTLGKHYINKHKGYYAISDSKM NIELNKETLNYLFSESLRYIKLFDEFLDLERDYLINHVLQFWKNDMYDLSLRKDLPELYL KTVMIDITLNIRYMPVEKLDIDQLQLSVKKYFAYISKLDSASVKSLKNEYRSYLQDNYLK KMNAEDDPRYKILDLIISKL The complete sample sequence of Utp12 is MVKSYQRFEQAAAFGVIASNANCVWIPASSGNSNGSGPGQLITSALEDVNIWDIKTGDLV SKLSDGLPPGASDARGAKPAECTYLEAHKDTDLLAVGYADGVIKVWDLMSKTVLLNFNGH KAAITLLQFDGTGTRLISGSKDSNIIVWDLVGEVGLYKLRSHKDSITGFWCQGEDWLIST SKDGMIKLWDLKTHQCIETHIAHTGECWGLAVKDDLLITTGTDSQVKIWKLDIENDKMGG KLTEMGIFEKQSKQRGLKIEFITNSSDKTSFFYIQNADKTIETFRIRKEEEIARGLKKRE KRLKEKGLTEEEIAKSIKESYSSFILHPFQTIRSLYKIKSASWTTVSSSKLELVLTTSSN TIEYYSIPYEKRDPTSPAPLKTHTIELQGQRTDVRSIDISDDNKLLATASNGSLKIWNIK THKCIRTFECGYALTCKFLPGGLLVILGTRNGELQLFDLASSSLLDTIEDAHDAAIWSLD LTSDGKRLVTGSADKTVKFWDFKVENSLVPGTKNKFLPVLKLHHDTTLELTDDILCVRVS PDDRYLAISLLDNTVKVFFLDSMKFYLSLYGHKLPVLSIDISFDSKMIITSSADKNIKIW GLDFGDCHKSLFAHQDSIMNVKFLPQSHNFFSCSKDAVVKYWDGEKFECIQKLYAHQSEV WALAVATDGGFVVSSSHDHSIRIWEETEDQVFLEEEKEKELEEQYEDTLLTSLEEGNGDD AFKADASGEGVEDEASGVHKQTLESLKAGERLMEALDLGIAEIEGLEAYNRDMKLWQRKK LGEAPIKPQGNAVLIAVNKTPEQYIMDTLLRIRMSQLEDALMVMPFSYVLKFLKFIDTVM QNKTLLHSHLPLICKNLFFIIKFNHKELVSQKNEELKLQINRVKTELRSALKSTEDDLGF NVQGLKFVKQQWNLRHNYEFVDEYDQQEKESNSARKRVFGTVI The complete sample sequence of Utp13 is MDLKTSYKGISLNPIYAGSSAVATVSENGKILATPVLDEINIIDLTPGSRKILHKISNED EQEITALKLTPDGQYLTYVSQAQLLKIFHLKTGKVVRSMKISSPSYILDADSTSTLLAVG GTDGSIIVVDIENGYITHSFKGHGGTISSLKFYGQLNSKIWLLASGDTNGMVKVWDLVKR KCLHTLQEHTSAVRGLDIIEVPDNDEPSLNLLSGGRDDIINLWDFNMKKKCKLLKTLPVN QQVESCGFLKDGDGKRIIYTAGGDAIFQLIDSESGSVLKRTNKPIEELFIIGVLPILSNS QMFLVLSDQTLQLINVEEDLKNDEDTIQVTSSIAGNHGIIADMRYVGPELNKLALATNSP SLRIIPVPDLSGPEASLPLDVEIYEGHEDLLNSLDATEDGLWIATASKDNTAIVWRYNEN SCKFDIYAKYIGHSAAVTAVGLPNIVSKGYPEFLLTASNDLTIKKWIIPKPTASMDVQII KVSEYTRHAHEKDINALSVSPNDSIFATASYDKTCKIWNLENGELEATLANHKRGLWDVS FCQYDKLLATSSGDKTVKIWSLDTFSVMKTLEGHTNAVQRCSFINKQKQLISCGADGLIK IWDCSSGECLKTLDGHNNRLWALSTMNDGDMIVSADADGVFQFWKDCTEQEIEEEQEKAK LQVEQEQSLQNYMSKGDWTNAFLLAMTLDHPMRLFNVLKRALGESRSRQDTEEGKIEVIF NEELDQAISILNDEQLILLMKRCRDWNTNAKTHTIAQRTIRCILMHHNIAKLSEIPGMVK IVDAIIPYTQRHFTRVDNLVEQSYILDYALVEMDKLF The complete sample sequence of Nop56 is MAPIEYLLFEEPTGYAVFKVKLQQDDIGSRLKEVQEQINDFGAFTKLIELVSFAPFKGAA EALENANDISEGLVSESLKAILDLNLPKASSKKKNITLAISDKNLGPSIKEEFPYVDCIS NELAQDLIRGVRLHGEKLFKGLQSGDLERAQLGLGHAYSRAKVKFSVQKNDNHIIQAIAL LDQLDKDINTFAMRVKEWYGWHFPELAKLVPDNYTFAKLVLFIKDKASLNDDSLHDLAAL LNEDSGIAQRVIDNARISMGQDISETDMENVCVFAQRVASLADYRRQLYDYLCEKMHTVA PNLSELIGEVIGARLISHAGSLTNLSKQAASTVQILGAEKALFRALKTKGNTPKYGLIYH SGFISKASAKNKGRISRYLANKCSMASRIDNYSEEPSNVFGSVLKKQVEQRLEFYNTGKP TLKNELAIQEAMELYNKDKPAAEVEETKEKESSKKRKLEDDDEEKKEKKEKKSKKEKKEK KEKKDKKEKKDKKEKKDKKKKSKD The complete sample sequence of Nop58 is MAYVLTETSAGYALLKASDKKIYKSSSLIQDLDSSDKVLKEFKIAAFSKFNSAANALEEA NSIIEGKVSSQLEKLLEEIKKDKKSTLIVSETKLANAINKLGLNFNVVSDAVTLDIYRAI KEYLPELLPGMSDNDLSKMSLGLAHSIGRHKLKFSADKVDVMIIQAIALLDDLDKELNTY AMRCKEWYGWHFPELAKIVTDSVAYARIILTMGIRSKASETDLSEILPEEIEERVKTAAE VSMGTEITQTDLDNINALAEQIVEFAAYREQLSNYLSARMKAIAPNLTQLVGELVGARLI AHSGSLISLAKSPASTIQILGAEKALFRALKTKHDTPKYGLLYHASLVGQATGKNKGKIA RVLAAKAAVSLRYDALAEDRDDSGDIGLESRAKVENRLSQLEGRDLRTTPKVVREAKKVE MTEARAYNADADTAKAASDSESDSDDEEEEKKEKKEKKRKRDDDEDSKDSKKAKKEKKDK KEKKEKKEKKEKKEKKEKKEKKSKKEKKEKK

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 5' ETS particle / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(HOCH2)3CNH21
2150 mMsodium chlorideNaClSodium chloride1
35 mMmagnesium chlorideMgCl21
45 mMbiotin1
55 mMputrescine1
61 mMspermidine1
70.03 %Triton X-1001
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 31.25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2750
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2RELION2.1particle selection
3RELION3particle selection
4SerialEMimage acquisition
6CTFFIND4.1.5CTF correction
7RELION3CTF correction
10Coot0.8.9model fitting
12PHENIXmodel refinement
13RELION2.1initial Euler assignment
14RELION3final Euler assignment
15RELION3classification
16RELION33D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 275080
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52629 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 5WLC

5wlc


Accession code: 5WLC / Source name: PDB / Type: experimental model

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