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- PDB-6r84: Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) -

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Basic information

Entry
Database: PDB / ID: 6r84
TitleYeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)
Components
  • (60S ribosomal protein ...) x 41
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • ABC transporter ATP-binding protein ARB1
  • Eukaryotic translation initiation factor 6
  • Protein VMS1,Vms1,Protein VMS1,Vms1
  • Ubiquitin-60S ribosomal protein L40
  • tRNA-Ala
KeywordsRIBOSOME / 60S ribosomal subunit / Vms1 / Arb1 / Tif6
Function / homology
Function and homology information


catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / aminoacyl-tRNA hydrolase activity / maturation of 5.8S rRNA / hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / aminoacyl-tRNA hydrolase activity / maturation of 5.8S rRNA / hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / protein quality control for misfolded or incompletely synthesized proteins / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein unfolding / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translational termination / ERAD pathway / maturation of LSU-rRNA / RNA endonuclease activity / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / cytosolic ribosome assembly / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome biogenesis / viral capsid / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / cytosolic large ribosomal subunit / Hydrolases; Acting on ester bonds / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / host cell nucleus / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
VLRF1/Vms1 / : / Bacteroidetes VLRF1 release factor / Vms1-like release factor 1 (VLRF1) domain profile. / : / ABC-transporter extension domain / ABC transporter / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Translation initiation factor IF6 ...VLRF1/Vms1 / : / Bacteroidetes VLRF1 release factor / Vms1-like release factor 1 (VLRF1) domain profile. / : / ABC-transporter extension domain / ABC transporter / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / : / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L1, conserved site / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L14e domain / Ribosomal protein L35Ae, conserved site / 60S ribosomal protein L19 / Ribosomal protein L14 / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L35 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L14 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L14, KOW motif / Ribosomal protein L1p/L10e family / Ribosomal protein L37ae / Ribosomal L37ae protein family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Pre-hexon-linking protein VIII / Large ribosomal subunit protein uL11A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13A / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / ABC transporter ATP-binding protein ARB1 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / tRNA endonuclease VMS1 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A / Large ribosomal subunit protein uL5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSu, T. / Izawa, T. / Cheng, J. / Yamashita, Y. / Berninghausen, O. / Inada, T. / Neupert, W. / Beckmann, R.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationNE 101/28-1 Germany
German Research FoundationGRK1721 Germany
German Research Foundationthe Graduate School of Quantitative Biosciences Munich (QBM) Germany
CitationJournal: Nature / Year: 2019
Title: Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis.
Authors: Ting Su / Toshiaki Izawa / Matthias Thoms / Yui Yamashita / Jingdong Cheng / Otto Berninghausen / F Ulrich Hartl / Toshifumi Inada / Walter Neupert / Roland Beckmann /
Abstract: Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes. After dissociation of ...Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes. After dissociation of ribosomes, the stalled tRNA-bound peptide remains associated with the 60S subunit and extended by Rqc2 by addition of C-terminal alanyl and threonyl residues (CAT tails), whereas Vms1 catalyses cleavage and release of the peptidyl-tRNA before or after addition of CAT tails. In doing so, Vms1 counteracts CAT-tailing of nuclear-encoded mitochondrial proteins that otherwise drive aggregation and compromise mitochondrial and cellular homeostasis. Here we present structural and functional insights into the interaction of Saccharomyces cerevisiae Vms1 with 60S subunits in pre- and post-peptidyl-tRNA cleavage states. Vms1 binds to 60S subunits with its Vms1-like release factor 1 (VLRF1), zinc finger and ankyrin domains. VLRF1 overlaps with the Rqc2 A-tRNA position and interacts with the ribosomal A-site, projecting its catalytic GSQ motif towards the CCA end of the tRNA, its Y285 residue dislodging the tRNA A73 for nucleolytic cleavage. Moreover, in the pre-state, we found the ABCF-type ATPase Arb1 in the ribosomal E-site, which stabilizes the delocalized A73 of the peptidyl-tRNA and stimulates Vms1-dependent tRNA cleavage. Our structural analysis provides mechanistic insights into the interplay of the RQC factors Vms1, Rqc2 and Arb1 and their role in the protection of mitochondria from the aggregation of toxic proteins.
History
DepositionMar 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Structure summary
Category: em_admin / pdbx_database_proc ...em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info / struct
Item: _em_admin.last_update / _em_admin.title ..._em_admin.last_update / _em_admin.title / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references
Category: citation / em_admin ...citation / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

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Assembly

Deposited unit
A: ABC transporter ATP-binding protein ARB1
R: Protein VMS1,Vms1,Protein VMS1,Vms1
X: Eukaryotic translation initiation factor 6
i: 60S ribosomal protein L34-A
J: 60S ribosomal protein L7-A
j: 60S ribosomal protein L35-A
K: 60S ribosomal protein L8-A
k: 60S ribosomal protein L36-A
7: 60S ribosomal protein L9-A
l: 60S ribosomal protein L37-A
M: 60S ribosomal protein L11-B
m: 60S ribosomal protein L38
N: 60S ribosomal protein L13-A
n: 60S ribosomal protein L39
O: 60S ribosomal protein L14-A
o: Ubiquitin-60S ribosomal protein L40
p: 60S ribosomal protein L15-A
Q: 60S ribosomal protein L16-A
5: 60S ribosomal protein L17-A
S: 60S ribosomal protein L18-A
s: 60S ribosomal protein L10
T: 60S ribosomal protein L19-A
U: 60S ribosomal protein L20-A
V: 60S ribosomal protein L21-A
W: 60S ribosomal protein L22-A
P: 60S ribosomal protein L12-A
r: 60S acidic ribosomal protein P0
x: 60S ribosomal protein L23-A
3: 5S rRNA
Y: 60S ribosomal protein L24-A
4: 5.8S rRNA
Z: 60S ribosomal protein L25
a: 60S ribosomal protein L26-A
B: tRNA-Ala
b: 60S ribosomal protein L27-A
C: 60S ribosomal protein L42-A
c: 60S ribosomal protein L28
D: 60S ribosomal protein L43-A
d: 60S ribosomal protein L29
E: 60S ribosomal protein L2-A
e: 60S ribosomal protein L30
F: 60S ribosomal protein L3
f: 60S ribosomal protein L31-A
G: 60S ribosomal protein L4-A
g: 60S ribosomal protein L32
H: 60S ribosomal protein L5
h: 60S ribosomal protein L33-A
I: 60S ribosomal protein L6-A
L: 60S ribosomal protein L1-A
1: 25S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,079,18151
Polymers2,079,11650
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules ARXor

#1: Protein ABC transporter ATP-binding protein ARB1 / ATP-binding cassette protein involved in ribosome biogenesis 1


Mass: 58604.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40024
#2: Protein Protein VMS1,Vms1,Protein VMS1,Vms1 / VCP/CDC48-associated mitochondrial stress-responsive protein 1


Mass: 48653.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VMS1, YDR049W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04311
#3: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 24156.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12522
#16: Protein Ubiquitin-60S ribosomal protein L40


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08
#27: Protein 60S acidic ribosomal protein P0 / A0 / L10e / Large ribosomal subunit protein uL10


Mass: 21715.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317

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60S ribosomal protein ... , 41 types, 41 molecules iJjKk7lMmNnOpQ5SsTUVWPxYZabCcD...

#4: Protein 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 12608.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P87262
#5: Protein 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 25240.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#6: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13811.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX84
#7: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#8: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11020.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05745
#9: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#10: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9746.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#11: Protein 60S ribosomal protein L11-B / L16 / Large ribosomal subunit protein uL5-B / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E757
#12: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8714.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49167
#13: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 21885.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12690
#14: Protein/peptide 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6227.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#15: Protein 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 14976.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL14A, YKL006W, YKL153 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#17: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#18: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#19: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#20: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX49
#21: Protein 60S ribosomal protein L10 / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI- ...L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25279.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805
#22: Protein 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 17447.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX82
#23: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX23
#24: Protein 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18148.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#25: Protein 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05749
#26: Protein 60S ribosomal protein L12-A / L15 / Large ribosomal subunit protein uL11-A / YL23


Mass: 16679.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX53
#28: Protein 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14362.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41
#30: Protein 60S ribosomal protein L24-A / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 7271.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449
#32: Protein 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#33: Protein 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14134.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#35: Protein 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15437.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H6
#36: Protein 60S ribosomal protein L42-A / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12115.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX27
#37: Protein 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#38: Protein 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 9981.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX25
#39: Protein 60S ribosomal protein L29 / Large ribosomal subunit protein eL29 / YL43


Mass: 6560.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05747
#40: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27217.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX45
#41: Protein 60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 10558.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#42: Protein 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#43: Protein 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12649.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#44: Protein 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#45: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14478.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#46: Protein 60S ribosomal protein L5 / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33633.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#47: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05744
#48: Protein 60S ribosomal protein L6-A / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 19869.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#49: Protein 60S ribosomal protein L1-A / L10a / Large ribosomal subunit protein uL1-A


Mass: 22974.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX43

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RNA chain , 4 types, 4 molecules 34B1

#29: RNA chain 5S rRNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1329886537
#31: RNA chain 5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1331532632
#34: RNA chain tRNA-Ala


Mass: 24502.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#50: RNA chain 25S rRNA


Mass: 1071848.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 1 types, 1 molecules

#51: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Vms1-60S ribosomal subunit complexRIBOSOMEYeast Vms1 bound 60S subunit in pre peptidyl-tRNA cleavage state containing Arb1#1-#500MULTIPLE SOURCES
260S ribosomal subunitRIBOSOME#1, #3-#14, #16-#501NATURAL
3Vms1COMPLEX#2, #151RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.8 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31832 / Symmetry type: POINT

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