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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 rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 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


Cdc48p-Npl4p-Vms1p AAA ATPase complex / nuclear protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / aminoacyl-tRNA hydrolase activity / 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) / 90S preribosome / preribosome, large subunit precursor / ribonucleoprotein complex assembly / response to cycloheximide ...Cdc48p-Npl4p-Vms1p AAA ATPase complex / nuclear protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / aminoacyl-tRNA hydrolase activity / 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) / 90S preribosome / preribosome, large subunit precursor / ribonucleoprotein complex assembly / response to cycloheximide / regulation of translational fidelity / negative regulation of mRNA splicing, via spliceosome / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA / ubiquitin-dependent ERAD pathway / assembly of large subunit precursor of preribosome / translational termination / maintenance of translational fidelity / modification-dependent protein catabolic process / large ribosomal subunit rRNA binding / cytoplasmic translation / rRNA processing / protein tag / macroautophagy / ribosome biogenesis / large ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / 5S rRNA binding / negative regulation of translation / ribosome / rRNA binding / nucleic acid binding / structural constituent of ribosome / protein ubiquitination / translation / ATPase activity / mRNA binding / endoplasmic reticulum membrane / ubiquitin protein ligase binding / mitochondrion / RNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Ribosomal protein L14p/L23e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 60S acidic ribosomal protein P0 ...Ribosomal protein L14p/L23e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 60S acidic ribosomal protein P0 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / ABC-transporter extension domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e superfamily / Ribosomal protein L1-like / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ankyrin repeat-containing domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L38e superfamily / Ribosomal protein L5, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L3, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L19/L19e conserved site / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L32e, conserved site / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L13e / Ribosomal protein L14 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L13 / bacteroidetes VLRF1 release factor / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L19e / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / eIF-6 family / Ribosomal protein L23 / KOW motif / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L27e protein family / Ribosomal L29e protein family / Ribosomal protein L5 / Ribosomal protein L31e / Ribosomal protein L32 / Ribosomal protein L35Ae / Ribosomal L29 protein / Ribosomal protein L36e / Ribosomal protein L37e / Ribosomal L38e protein family / Ribosomal L39 protein / Ribosomal L40e family / Ribosomal L15 / Ribosomal protein L10 / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L16p/L10e / ribosomal L5P family C-terminus / Ribosomal protein L1p/L10e family / Ribosomal protein L22e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily
60S ribosomal protein L15-A / 60S ribosomal protein L29 / 60S ribosomal protein L36-A / 60S ribosomal protein L4-A / 60S ribosomal protein L33-A / 60S ribosomal protein L26-A / 60S ribosomal protein L17-A / 60S ribosomal protein L7-A / 60S acidic ribosomal protein P0 / 60S ribosomal protein L39 ...60S ribosomal protein L15-A / 60S ribosomal protein L29 / 60S ribosomal protein L36-A / 60S ribosomal protein L4-A / 60S ribosomal protein L33-A / 60S ribosomal protein L26-A / 60S ribosomal protein L17-A / 60S ribosomal protein L7-A / 60S acidic ribosomal protein P0 / 60S ribosomal protein L39 / 60S ribosomal protein L25 / 60S ribosomal protein L24-A / 60S ribosomal protein L28 / 60S ribosomal protein L22-A / 60S ribosomal protein L31-A / 60S ribosomal protein L27-A / ORF2 / 60S ribosomal protein L3 / 60S ribosomal protein L8-A / 60S ribosomal protein L5 / 60S ribosomal protein L16-A / 60S ribosomal protein L14-A / 60S ribosomal protein L32 / ABC transporter ATP-binding protein ARB1 / 60S ribosomal protein L10 / 60S ribosomal protein L37-A / 60S ribosomal protein L38 / 60S ribosomal protein L34-A / 60S ribosomal protein L6-A / 60S ribosomal protein L21-A / Protein VMS1 / 60S ribosomal protein L13-A / 60S ribosomal protein L30 / 60S ribosomal protein L11-B / gb:1329886537: / gb:1331532632: / 60S ribosomal protein L35-A / 60S ribosomal protein L19-A / 60S ribosomal protein L12-A / 60S ribosomal protein L18-A / 60S ribosomal protein L2-A / 60S ribosomal protein L1-A / 60S ribosomal protein L23-A / 60S ribosomal protein L42-A / 60S ribosomal protein L43-A / 60S ribosomal protein L20-A / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L9-A
Biological speciesSaccharomyces cerevisiae (baker'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.
Validation Report
SummaryFull reportAbout validation report
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
Water0
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 (baker'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 (baker's yeast)
Gene: VMS1, YDR049W / Production host: Saccharomyces cerevisiae (baker'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 (baker'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 (baker'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 (baker's yeast) / References: UniProt: P05317

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

#4: Protein 60S ribosomal protein L34-A / Ribosome / 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 (baker's yeast) / References: UniProt: P87262
#5: Protein 60S ribosomal protein L7-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05737
#6: Protein 60S ribosomal protein L35-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX84
#7: Protein 60S ribosomal protein L8-A / Ribosome / 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 (baker's yeast) / References: UniProt: P17076
#8: Protein 60S ribosomal protein L36-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05745
#9: Protein 60S ribosomal protein L9-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05738
#10: Protein 60S ribosomal protein L37-A / Ribosome / 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 (baker's yeast) / References: UniProt: P49166
#11: Protein 60S ribosomal protein L11-B / Ribosome / 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 (baker'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 (baker's yeast) / References: UniProt: P49167
#13: Protein 60S ribosomal protein L13-A / Ribosome / 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 (baker'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 (baker's yeast) / References: UniProt: P04650
#15: Protein 60S ribosomal protein L14-A / Ribosome / 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 (baker's yeast)
Gene: RPL14A, YKL006W, YKL153 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#17: Protein 60S ribosomal protein L15-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05748
#18: Protein 60S ribosomal protein L16-A / Ribosome / 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 (baker's yeast) / References: UniProt: P26784
#19: Protein 60S ribosomal protein L17-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05740
#20: Protein 60S ribosomal protein L18-A / Ribosome / 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 (baker'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 (baker's yeast) / References: UniProt: P41805
#22: Protein 60S ribosomal protein L19-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX82
#23: Protein 60S ribosomal protein L20-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX23
#24: Protein 60S ribosomal protein L21-A / Ribosome / 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 (baker's yeast) / References: UniProt: Q02753
#25: Protein 60S ribosomal protein L22-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05749
#26: Protein 60S ribosomal protein L12-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX53
#28: Protein 60S ribosomal protein L23-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX41
#30: Protein 60S ribosomal protein L24-A / Ribosome / 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 (baker'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 (baker's yeast) / References: UniProt: P04456
#33: Protein 60S ribosomal protein L26-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05743
#35: Protein 60S ribosomal protein L27-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0C2H6
#36: Protein 60S ribosomal protein L42-A / Ribosome / 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 (baker'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 (baker's yeast) / References: UniProt: P02406
#38: Protein 60S ribosomal protein L43-A / Ribosome / 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 (baker'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 (baker's yeast) / References: UniProt: P05747
#40: Protein 60S ribosomal protein L2-A / Ribosome / 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 (baker'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 (baker'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 (baker's yeast) / References: UniProt: P14126
#43: Protein 60S ribosomal protein L31-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0C2H8
#44: Protein 60S ribosomal protein L4-A / Ribosome / 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 (baker'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 (baker'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 (baker's yeast) / References: UniProt: P26321
#47: Protein 60S ribosomal protein L33-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05744
#48: Protein 60S ribosomal protein L6-A / Ribosome / 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 (baker's yeast) / References: UniProt: Q02326
#49: Protein 60S ribosomal protein L1-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX43

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RNA chain , 4 types, 4 molecules 34B1

#29: RNA chain 5S rRNA / 5S ribosomal RNA


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


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker'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 (baker'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 (baker's yeast)

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Non-polymers , 1 types, 1 molecules

#51: Chemical ChemComp-ZN / ZINC ION / Zinc


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 Arb11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 500MULTIPLE SOURCES
260S ribosomal subunitRIBOSOME1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 501NATURAL
3Vms1COMPLEX2,151RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (baker's yeast)4932
32Saccharomyces cerevisiae (baker's yeast)4932
Source (recombinant)Organism: Saccharomyces cerevisiae (baker'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 FIELDBright-field microscopy
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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