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- EMDB-4751: Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) -

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Basic information

Entry
Database: EMDB / ID: EMD-4751
TitleYeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)
Map data
SampleVms1-60S ribosomal subunit complex
  • 60S ribosomal subunit
  • Vms1
  • ABC transporter ATP-binding protein ARB1
  • Protein VMS1,Vms1,Protein VMS1,Vms1
  • Eukaryotic translation initiation factor 6
  • (60S ribosomal protein ...) x 41
  • Ubiquitin-60S ribosomal protein L40
  • 60S acidic ribosomal protein P0
  • (nucleic-acidNucleic acid) x 4
  • ligand
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 / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / maturation of 5.8S rRNA / pre-mRNA 5'-splice site binding / aminoacyl-tRNA hydrolase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus ...Cdc48p-Npl4p-Vms1p AAA ATPase complex / nuclear protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / maturation of 5.8S rRNA / pre-mRNA 5'-splice site binding / aminoacyl-tRNA hydrolase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / Termination of translesion DNA synthesis / response to cycloheximide / preribosome, large subunit precursor / 90S preribosome / ribonucleoprotein complex assembly / ribosomal large subunit binding / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal large subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit export from nucleus / regulation of translational fidelity / 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 / mature ribosome assembly / translational termination / translation initiation factor activity / assembly of large subunit precursor of preribosome / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / ATP hydrolysis activity / protein tag / rRNA processing / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / ribosome biogenesis / 5S rRNA binding / negative regulation of translation / protein ubiquitination / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / ubiquitin protein ligase binding / nucleolus / endoplasmic reticulum membrane / mitochondrion / RNA binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Bacteroidetes VLRF1 release factor / VLRF1/Vms1 / ABC-transporter extension domain / ABC transporter / Translation initiation factor IF6 / translation initiation factor 6 / eIF-6 family / 60S acidic ribosomal protein P0 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain ...Bacteroidetes VLRF1 release factor / VLRF1/Vms1 / ABC-transporter extension domain / ABC transporter / Translation initiation factor IF6 / translation initiation factor 6 / eIF-6 family / 60S acidic ribosomal protein P0 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L22e superfamily / Ribosomal protein L22e / Ribosomal L22e protein family / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal L38e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L29e protein family / Ribosomal protein L29e / Ribosomal L40e family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L19, eukaryotic / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L18e / Ribosomal protein L27e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L6e signature. / Ribosomal protein L23, N-terminal domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L30e signature 1. / Ribosomal protein L7A/L8 / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e / Ribosomal protein L34Ae / Ribosomal protein L36e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e signature 2. / Ribosomal protein L35Ae signature. / Ribosomal protein L30e, conserved site / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal Protein L6, KOW domain / Ribosomal protein L30/YlxQ / Ribosomal protein L7, eukaryotic / Ribosomal protein L24e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L36e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / 60S ribosomal protein L4 C-terminal domain / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L18e signature. / Ribosomal protein L18e, conserved site / Ribosomal protein L6e / Ribosomal protein L7/L30 / Ribosomal protein L10e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L10e signature. / Ribosomal_L19e / Ribosomal protein L10e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e superfamily / Ribosomal protein L14 / Ribosomal protein L19e / Ribosomal protein L44e / 60S ribosomal protein L19 / Ribosomal protein L44 / Ribosomal protein L14e domain / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal L37ae protein family / Ribosomal protein L37ae / Ribosomal protein L31e signature. / Ribosomal protein L31e, conserved site / Ribosomal protein L1, conserved site
Similarity search - Domain/homology
60S ribosomal protein L12-A / 60S ribosomal protein L19-A / 60S ribosomal protein L35-A / 60S ribosomal protein L4-A / 60S ribosomal protein L30 / 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 L12-A / 60S ribosomal protein L19-A / 60S ribosomal protein L35-A / 60S ribosomal protein L4-A / 60S ribosomal protein L30 / 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 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L13-A / 60S ribosomal protein L18-A / 60S ribosomal protein L2-A / 60S ribosomal protein L1-A / 60S ribosomal protein L33-A / 60S ribosomal protein L28 / 60S ribosomal protein L24-A / 60S ribosomal protein L25 / 60S ribosomal protein L39 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L7-A / 60S ribosomal protein L9-A / 60S ribosomal protein L17-A / 60S ribosomal protein L26-A / 60S ribosomal protein L36-A / 60S ribosomal protein L23-A / 60S ribosomal protein L29 / 60S ribosomal protein L15-A / 60S ribosomal protein L22-A / 60S ribosomal protein L27-A / 60S ribosomal protein L31-A / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L20-A / 60S ribosomal protein L43-A / 60S ribosomal protein L42-A / 60S ribosomal protein L11-B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle 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, 3 items
OrganizationGrant numberCountry
German Research FoundationNE 101/28-1 Germany
German Research Foundationthe Graduate School of Quantitative Biosciences Munich (QBM) Germany
German Research FoundationGRK1721 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, 2019-
Header (metadata) releaseJun 26, 2019-
Map releaseJun 26, 2019-
UpdateJul 10, 2019-
Current statusJul 10, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r84
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4751.map.gz / Format: CCP4 / Size: 236.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 396 pix.
= 429.264 Å
1.08 Å/pix.
x 396 pix.
= 429.264 Å
1.08 Å/pix.
x 396 pix.
= 429.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.05
Minimum - Maximum-0.38242877 - 0.56043845
Average (Standard dev.)0.00049947883 (±0.016553828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions396396396
Spacing396396396
CellA=B=C: 429.264 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z396396396
origin x/y/z0.0000.0000.000
length x/y/z429.264429.264429.264
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS396396396
D min/max/mean-0.3820.5600.000

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Supplemental data

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Sample components

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Entire Vms1-60S ribosomal subunit complex

EntireName: Vms1-60S ribosomal subunit complex
Details: Yeast Vms1 bound 60S subunit in pre peptidyl-tRNA cleavage state containing Arb1
Number of Components: 54

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Component #1: protein, Vms1-60S ribosomal subunit complex

ProteinName: Vms1-60S ribosomal subunit complex
Details: Yeast Vms1 bound 60S subunit in pre peptidyl-tRNA cleavage state containing Arb1
Recombinant expression: No

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Component #2: protein, 60S ribosomal subunit

ProteinName: 60S ribosomal subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, Vms1

ProteinName: Vms1 / Recombinant expression: No
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, ABC transporter ATP-binding protein ARB1

ProteinName: ABC transporter ATP-binding protein ARB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.604406 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, Protein VMS1,Vms1,Protein VMS1,Vms1

ProteinName: Protein VMS1,Vms1,Protein VMS1,Vms1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.653203 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, Eukaryotic translation initiation factor 6

ProteinName: Eukaryotic translation initiation factor 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.15615 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.608831 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.240377 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.811444 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.814998 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.020063 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.605061 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.746199 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, 60S ribosomal protein L11-B

ProteinName: 60S ribosomal protein L11-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.266082 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.714363 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.885234 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.227444 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.976794 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #19: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.032321 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.351162 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.028951 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.458322 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478059 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.279271 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.447391 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.148066 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.263863 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #29: protein, 60S ribosomal protein L12-A

ProteinName: 60S ribosomal protein L12-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.679318 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #30: protein, 60S acidic ribosomal protein P0

ProteinName: 60S acidic ribosomal protein P0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.715035 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #31: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.362755 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #32: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #33: protein, 60S ribosomal protein L24-A

ProteinName: 60S ribosomal protein L24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.27155 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #34: nucleic-acid, 5.8S rRNA

nucleic acidName: 5.8S rRNA5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUUU
MassTheoretical: 50.682922 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #35: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.771176 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #36: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.134588 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #37: nucleic-acid, tRNA-Ala

nucleic acidName: tRNA-Ala / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGCGUGUGG CGUAGUCGGU AGCGCGCUCC CUUAGCAUGG GAGAGGUCUC CGGUUCGAUU CCGGACUCGU CCGCCA
MassTheoretical: 24.502477 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #38: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.437166 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #39: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.115462 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #40: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.630471 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #41: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.981756 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #42: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.560688 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #43: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.217289 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #44: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.558344 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #45: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.719602 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #46: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.649754 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #47: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.027926 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #48: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.478054 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #49: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.633633 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #50: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.045935 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #51: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.869369 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #52: protein, 60S ribosomal protein L1-A

ProteinName: 60S ribosomal protein L1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.974033 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #53: nucleic-acid, 25S rRNA

nucleic acidName: 25S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UUGACCUCAA AUCAGGUAGG AGUACCCGCU GAACUUAAGC AUAUCAAUAA GCGGAGGAAA AGAAACCAAC CGGGAUUGCC UUAGUAACGG CGAGUGAAGC GGCAAAAGCU CAAAUUUGAA AUCUGGUACC UUCGGUGCCC GAGUUGUAAU UUGGAGAGGG CAACUUUGGG ...Sequence:
UUGACCUCAA AUCAGGUAGG AGUACCCGCU GAACUUAAGC AUAUCAAUAA GCGGAGGAAA AGAAACCAAC CGGGAUUGCC UUAGUAACGG CGAGUGAAGC GGCAAAAGCU CAAAUUUGAA AUCUGGUACC UUCGGUGCCC GAGUUGUAAU UUGGAGAGGG CAACUUUGGG GCCGUUCCUU GUCUAUGUUC CUUGGAACAG GACGUCAUAG AGGGUGAGAA UCCCGUGUGG CGAGGAGUGC GGUUCUUUGU AAAGUGCCUU CGAAGAGUCG AGUUGUUUGG GAAUGCAGCU CUAAGUGGGU GGUAAAUUCC AUCUAAAGCU AAAUAUUGGC GAGAGACCGA UAGCGAACAA GUACAGUGAU GGAAAGAUGA AAAGAACUUU GAAAAGAGAG UGAAAAAGUA CGUGAAAUUG UUGAAAGGGA AGGGCAUUUG AUCAGACAGG CCAGCAUCAG UUUUGGUGGC AGGAUAAAUC CAUAGGAAUG UAGCUUGCCU CGGUAAGUAU UAUAGCCUGU GGGAAUACUG CCAGCUGGGA CUGAGGACUG CGACGUAAGU CAAGGAUGCU GGCAUAAUGG UUAUAUGCCG CCCGUCUUGA AACACGGACC AAGGAGUCUA ACGUCUAUGC GAGUGUUUGG GUGUAAAACC CAUACGCGUA AUGAAAGUGA ACGUAGGUUG GGGCCUCGCA AGAGGUGCAC AAUCGACCGA UCCUGAUGUC UUCGGAUGGA UUUGAGUAAG AGCAUAGCUG UUGGGACCCG AAAGAUGGUG AACUAUGCCU GAAUAGGGUG AAGCCAGAGG AAACUCUGGU GGAGGCUCGU AGCGGUUCUG ACGUGCAAAU CGAUCGUCGA AUUUGGGUAU AGGGGCGAAA GACUAAUCGA ACCAUCUAGU AGCUGGUUCC UGCCGAAGUU UCCCUCAGGA UAGCAGAAGC UCGUAUCAGU UUUAUGAGGU AAAGCGAAUG AUUAGAGGUU CCGGGGUCGA AAUGACCUUG ACCUAUUCUC AAACUUUAAA UAUGUAAGAA GUCCUUGUUA CUUAAUUGAA CGUGGACAUU UGAAUGAAGA GCUUUUAGUG GGCCAUUUUU GGUAAGCAGA ACUGGCGAUG CGGGAUGAAC CGAACGUAGA GUUAAGGUGC CGGAAUACAC GCUCAUCAGA CACCACAAAA GGUGUUAGUU CAUCUAGACA GCCGGACGGU GGCCAUGGAA GUCGGAAUCC GCUAAGGAGU GUGUAACAAC UCACCGGCCG AAUGAACUAG CCCUGAAAAU GGAUGGCGCU CAAGCGUGUU ACCUAUACUC UACCGUCAGG GUUGAUAUGA UGCCCUGACG AGUAGGCAGG CGUGGAGGUC AGUGACGAAG CCUAGACCGU AAGGUCGGGU CGAACGGCCU CUAGUGCAGA UCUUGGUGGU AGUAGCAAAU AUUCAAAUGA GAACUUUGAA GACUGAAGUG GGGAAAGGUU CCACGUCAAC AGCAGUUGGA CGUGGGUUAG UCGAUCCUAA GAGAUGGGGA AGCUCCGUUU CAAAGGCCUG AUUUUAUGCA GGCCACCAUC GAAAGGGAAU CCGGUUAAGA UUCCGGAACC UGGAUAUGGA UUCUUCACGG UAACGUAACU GAAUGUGGAG ACGUCGGCGC GAGCCCUGGG AGGAGUUAUC UUUUCUUCUU AACAGCUUAU CACCCCGGAA UUGGUUUAUC CGGAGAUGGG GUCUUAUGGC UGGAAGAGGC CAGCACCUUU GCUGGCUCCG GUGCGCUUGU GACGGCCCGU GAAAAUCCAC AGGAAGGAAU AGUUUUCAUG CCAGGUCGUA CUGAUAACCG CAGCAGGUCU CCAAGGUGAA CAGCCUCUAG UUGAUAGAAU AAUGUAGAUA AGGGAAGUCG GCAAAAUAGA UCCGUAACUU CGGGAUAAGG AUUGGCUCUA AGGGUCGGGU AGUGAGAGCC UUGGUCAGAC GCAGCGGGCG UGCUUGUGGA CUGCUUGGUG GGGCUUGCUC UGCUAGGCGG ACUACUUGCG UGCCUUGUUG UAGACGGCCU UGGUCUUGCU ACACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.071848375 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #54: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 2.8 e/Å2 / Illumination Mode: SPOT SCAN
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 31832
3D reconstructionResolution: 3.6 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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