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- EMDB-3551: Structure of the yeast mitochondrial ribosome - Class A -

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Basic information

Entry
Database: EMDB / ID: EMD-3551
TitleStructure of the yeast mitochondrial ribosome - Class A
Map data
Sampleyeast mitochondrial ribosome - Class A:
(nucleic-acidNucleic acid) x 3 / uL2m / uL3m / uL4m / uL5m / uL6m / bL9m / uL13m / uL14m / uL15m ...(nucleic-acidNucleic acid) x 3 / uL2m / uL3m / uL4m / uL5m / uL6m / bL9m / uL13m / uL14m / uL15m / uL16m / bL17m / bL19m / bL21m / uL22m / uL23m / uL24m / bL27m / bL28m / uL29m / uL30m / bL31m / bL32m / bL33m / bL34m / bL35m / bL36m / mL38 / mL40 / mL41 / mL43 / mL44 / mL46 / mL49 / mL50 / mL57 / mL58 / mL59 / mL60 / mL67 / bS1m / uS2m / uS3m / uS4m / uS5m / bS6m / uS7m / uS8m / uS9m / uS10m / uS11m / uS12m / uS13m / uS14m / uS15m / bS16m / uS17m / bS18m / uS19m / bS21m / mS23 / mS26 / mS29 / mS33 / mS35 / mS37 / mS38 / mS41 / mS42 / mS43 / mS44 / mS45 / mS46 / mS47 / (unknown protein sequence ...) x 2 / (ligand) x 4
Function / homology
Function and homology information


Branched-chain amino acid catabolism / 3-hydroxyisobutyryl-CoA hydrolase / positive regulation of mitochondrial DNA replication / peptidyltransferase activity / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / peptidase inhibitor activity / regulation of Ras protein signal transduction / mitochondrial small ribosomal subunit / mitochondrial large ribosomal subunit ...Branched-chain amino acid catabolism / 3-hydroxyisobutyryl-CoA hydrolase / positive regulation of mitochondrial DNA replication / peptidyltransferase activity / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / peptidase inhibitor activity / regulation of Ras protein signal transduction / mitochondrial small ribosomal subunit / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial genome maintenance / integral component of mitochondrial inner membrane / mitochondrial translation / recombinase activity / ribonuclease III activity / primary miRNA processing / branched-chain amino acid catabolic process / production of siRNA involved in RNA interference / pre-miRNA processing / fatty acid beta-oxidation / RNA processing / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / positive regulation of translational fidelity / ribosome assembly / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome biogenesis / mRNA processing / phospholipid binding / cytosolic large ribosomal subunit / single-stranded DNA binding / large ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / ribosome binding / double-stranded RNA binding / cellular response to oxidative stress / mitochondrial inner membrane / transferase activity / ribosome / negative regulation of translation / rRNA binding / structural constituent of ribosome / DNA recombination / translation / mRNA binding / GTP binding / regulation of transcription, DNA-templated / mitochondrion / RNA binding / DNA binding / nucleus / metal ion binding / cytoplasm
Ribosomal L18e/L15P superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily ...Ribosomal L18e/L15P superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S10 domain / Ribosomal protein L46, N-terminal / Ribosomal protein L21-like / ClpP/crotonase-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / 54S ribosomal protein L36, yeast / L28p-like / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / L21-like superfamily / Ribosomal L32p protein family / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Ribosomal protein S24/S35, mitochondrial, conserved domain / Ribosomal protein S23, mitochondrial, fungi / Ribosomal protein MRP10, mitochondrial / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein L50, mitochondria / Enoyl-CoA hydratase/isomerase, conserved site / IGR protein motif / Ribosomal protein L27/L41, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein L18e/L15P / Manganese/iron superoxide dismutase, C-terminal / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S35, mitochondrial / Thioredoxin-like superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Mitochondrial ribosomal protein S25 / Ribosomal protein L36 / Ribosomal protein S14p/S29e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein L30p/L7e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10p/S20e / Ribosomal protein L6 / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S13/S18 / Ribosomal protein L34 / Ribosomal protein L14p/L23e / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal protein S16 / Ribosomal L27 protein / Ribosomal protein S18 / Phosphatidylethanolamine-binding protein / Ribosomal protein S21 / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein S6
37S ribosomal protein S35, mitochondrial / 54S ribosomal protein YmL6, mitochondrial / Mitochondrial 37S ribosomal protein S27 / 37S ribosomal protein S7, mitochondrial / 37S ribosomal protein S26, mitochondrial / 37S ribosomal protein S18, mitochondrial / 54S ribosomal protein L40, mitochondrial / 37S ribosomal protein MRP21, mitochondrial / 54S ribosomal protein L49, mitochondrial / 37S ribosomal protein S25, mitochondrial ...37S ribosomal protein S35, mitochondrial / 54S ribosomal protein YmL6, mitochondrial / Mitochondrial 37S ribosomal protein S27 / 37S ribosomal protein S7, mitochondrial / 37S ribosomal protein S26, mitochondrial / 37S ribosomal protein S18, mitochondrial / 54S ribosomal protein L40, mitochondrial / 37S ribosomal protein MRP21, mitochondrial / 54S ribosomal protein L49, mitochondrial / 37S ribosomal protein S25, mitochondrial / 37S ribosomal protein RSM18, mitochondrial / Protein FYV4, mitochondrial / 37S ribosomal protein S9, mitochondrial / 54S ribosomal protein L16, mitochondrial / 37S ribosomal protein S12, mitochondrial / 54S ribosomal protein L50, mitochondrial / 37S ribosomal protein RSM28, mitochondrial / 37S ribosomal protein S19, mitochondrial / 37S ribosomal protein S8, mitochondrial / 54S ribosomal protein L36, mitochondrial / 54S ribosomal protein L35, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L51, mitochondrial / 54S ribosomal protein L34, mitochondrial / 37S ribosomal protein S24, mitochondrial / 37S ribosomal protein S17, mitochondrial / 54S ribosomal protein L22, mitochondrial / 37S ribosomal protein S10, mitochondrial / 37S ribosomal protein MRP51, mitochondrial / 37S ribosomal protein S16, mitochondrial / 54S ribosomal protein L13, mitochondrial / 37S ribosomal protein S23, mitochondrial / 37S ribosomal protein SWS2, mitochondrial / 54S ribosomal protein bL35m / 54S ribosomal protein L39, mitochondrial / 54S ribosomal protein L31, mitochondrial / 54S ribosomal protein L17, mitochondrial / 54S ribosomal protein L33, mitochondrial / 54S ribosomal protein IMG1, mitochondrial / 54S ribosomal protein L32, mitochondrial / 54S ribosomal protein L25, mitochondrial / 54S ribosomal protein L20, mitochondrial / 54S ribosomal protein L8, mitochondrial / 37S ribosomal protein S28, mitochondrial / 37S ribosomal protein PET123, mitochondrial / 37S ribosomal protein NAM9, mitochondrial / 54S ribosomal protein L2, mitochondrial / 37S ribosomal protein MRP13, mitochondrial / 37S ribosomal protein MRP2, mitochondrial / 37S ribosomal protein MRP1, mitochondrial / Ribosomal protein VAR1, mitochondrial / 37S ribosomal protein MRP10, mitochondrial / 54S ribosomal protein RTC6, mitochondrial / 54S ribosomal protein IMG2, mitochondrial / 37S ribosomal protein MRP17, mitochondrial / 54S ribosomal protein L28, mitochondrial / 54S ribosomal protein L3, mitochondrial / 54S ribosomal protein L27, mitochondrial / 54S ribosomal protein L24, mitochondrial / 54S ribosomal protein L15, mitochondrial / 54S ribosomal protein L10, mitochondrial / 54S ribosomal protein L7, mitochondrial / 54S ribosomal protein L4, mitochondrial / 54S ribosomal protein L38, mitochondrial / 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial / 37S ribosomal protein S5, mitochondrial / 54S ribosomal protein L6, mitochondrial / 37S ribosomal protein MRP4, mitochondrial / 54S ribosomal protein RML2, mitochondrial / 54S ribosomal protein L41, mitochondrial / Mitochondrial mRNA-processing protein COX24 / 54S ribosomal protein L9, mitochondrial / 54S ribosomal protein L23, mitochondrial
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsDesai N / Brown A / Amunts A / Ramakrishnan V
CitationJournal: Science / Year: 2017
Title: The structure of the yeast mitochondrial ribosome.
Authors: Nirupa Desai / Alan Brown / Alexey Amunts / V Ramakrishnan /
Abstract: Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the ...Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.
Validation ReportPDB-ID: 5mrc

SummaryFull reportAbout validation report
DateDeposition: Dec 22, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Feb 15, 2017 / Update: Feb 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.146
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.146
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5mrc
  • Surface level: 0.146
  • 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_3551.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 330 pix.
= 442.2 Å
1.34 Å/pix.
x 330 pix.
= 442.2 Å
1.34 Å/pix.
x 330 pix.
= 442.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.146 / Movie #1: 0.146
Minimum - Maximum-0.667045 - 1.0444973
Average (Standard dev.)-0.00037892122 (±0.046740957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 442.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z442.200442.200442.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.6671.044-0.000

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Supplemental data

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Sample components

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Entire yeast mitochondrial ribosome - Class A

EntireName: yeast mitochondrial ribosome - Class A / Number of components: 83

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Component #1: protein, yeast mitochondrial ribosome - Class A

ProteinName: yeast mitochondrial ribosome - Class A / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: nucleic-acid, 21S ribosomal RNA

nucleic acidName: 21S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUAAAAAGUA GAAUAAUAGA UUUGAAAUAU UUAUUAUAUA GAUUUAAAGA GAUAAUCAUG GAGUAUAAUA AUUAAAUUUA AUAAAUUUAA UAUAACUAUU AAUAGAAUUA GGUUACUAAU AAAUUAAUAA CAAUUAAUUU UAAAACCUAA AGGUAAACCU UUAUAUUAAU AAUGUUAUUU UUUAUUAUUU UUAUAAUAAG AAUAAUUAUU AAUAAUAAUA AACUAAGUGA ACUGAAACAU CUAAGUAACU UAAGGAUAAG AAAUCAACAG AGAUAUUAUG AGUAUUGGUG AGAGAAAAUA AUAAAGGUCU AAUAAGUAUU AUGUGAAAAA AAUGUAAGAA AAUAGGAUAA CAAAUUCUAA GACUAAAUAC UAUUAAUAAG UAUAGUAAGU ACCGUAAGGG AAAGUAUGAA AAUGAUUAUU UUAUAAGCAA UCAUGAAUAU AUUAUAUUAU AUUAAUGAUG UACCUUUUGU AUAAUGGGUC AGCAAGUAAU UAAUAUUAGU AAAACAAUAA GUUAUAAAUA AAUAGAAUAA UAUAUAUAUA UAAAAAAAUA UAUUAAAAUA UUUAAUUAAU AUUAAUUGAC CCGAAAGCAA ACGAUCUAAC UAUGAUAAGA UGGAUAAACG AUCGAACAGG UUGAUGUUGC AAUAUCAUCU GAUUAAUUGU GGUUAGUAGU GAAAGACAAA UCUGGUUUGC AGAUAGCUGG UUUUCUAUGA AAUAUAUGUA AGUAUAGCCU UUAUAAAUAA UAAUUAUUAU AUAAUAUUAU AUUAAUAUUA UAUAAAGAAU GGUACAGCAA UUAAUAUAUA UUAGGGAACU AUUAAAGUUU UAUUAAUAAU AUUAAAUCUC GAAAUAUUUA AUUAUAUAUA AUAAAGAGUC AGAUUAUGUG CGAUAAGGUA AAUAAUCUAA AGGGAAACAG CCCAGAUUAA GAUAUAAAGU UCCUAAUAAA UAAUAAGUGA AAUAAAUAUU AAAAUAUUAU AAUAUAAUCA GUUAAUGGGU UUGACAAUAA CCAUUUUUUA AUGAACAUGU AACAAUGCAC UGAUUUAUAA UAAAUAAAAA AAAAUAAUAU UUAAAAUCAA AUAUAUAUAU AUUUGUUAAU AGAUAAUAUA CGGAUCUUAA UAAUAAGAAU UAUUUAAUUC CUAAUAUGGA AUAUUAUAUU UUUAUAAUAA AAAUAUAAAU ACUGAAUAUC UAAAUAUUAU UAUUACUUUU UUUUUAAUAA UAAUAAUAUG GUAAUAGAAC AUUUAAUGAU AAUAUAUAUU AGUUAUUAAU UAAUAUAUGU AUUAAUUAAA UAGAGAAUGC UGACAUGAGU AACGAAAAAA AGGUAUAAAC CUUUUCACCU AAAACAUAAG GUUUAACUAU AAAAGUACGG CCCCUAAUUA AAUUAAUAAA AAUAUAAAUA UAUUUAAGAU GGGAUAAUCU AUAUUAAUAA AAAUUUAUCU UAAAAUAUAU AUAUUAUUAA UAAUUAUAUU AAUUAAUUAA UAAUAUAUAU AAUUAUAUUA UAUAUUAUAU AUUUUUUAUA UAAUAUAAAC UAAUAAAGAU CAGGAAAUAA UUAAUGUAUA CCGUAAUGUA GACCGACUCA GGUAUGUAAG UAGAGAAUAU GAAGGUGAAU UAGAUAAUUA AAGGGAAGGA ACUCGGCAAA GAUAGCUCAU AAGUUAGUCA AUAAAGAGUA AUAAGAACAA AGUUGUACAA CUGUUUACUA AAAACACCGC ACUUUGCAGA AACGAUAAGU UUAAGUAUAA GGUGUGAACU CUGCUCCAUG CUUAAUAUAU AAAUAAAAUU AUUUAACGAU AAUUUAAUUA AAUUUAGGUA AAUAGCAGCC UUAUUAUGAG GGUUAUAAUG UAGCGAAAUU CCUUGGCCUA UAAUUGAGGU CCCGCAUGAA UGACGUAAUG AUACAACAAC UGUCUCCCCU UUAAGCUAAG UGAAAUUGAA AUCGUAGUGA AGAUGCUAUG UACCUUCAGC AAGACGGAAA GACCCUAUGC AGCUUUACUG UAAUUAGAUA GAUCGAAUUA UUGUUUAUUA UAUUCAGCAU AUUAAGUAAU CCUAUUAUUA GGUAAUCGUU UAGAUAUUAA UGAGAUACUU AUUAUAAUAU AAUGAUAAUU CUAAUCUUAU AAAUAAUUAU UAUUAUUAUU AUUAAUAAUA AUAAUAUGCU UUCAAGCAUA GUGAUAAAAC AUAUUUAUAU GAUAAUCACU UUACUUAAUA GAUAUAAUUC UUAAGUAAUA UAUAAUAUAU AUUUUAUAUA UAUUAUAUAU AAUAUAAGAG ACAAUCUCUA AUUGGUAGUU UUGAUGGGGC GUCAUUAUCA GCAAAAGUAU CUGAAUAAGU CCAUAAAUAA AUAUAUAAAA UUAUUGAAUA AAAAAAAAAU AAUAUAUAUU AUAUAUAUUA AUUAUAAAUU GAAAUAUGUU UAUAUAAAUU UAUAUUUAUU GAAUAUAUUU UAGUAAUAGA UAAAAAUAUG UACAGUAAAA UUGUAAGGAA AACAAUAAUA ACUUUCUCCU CUCUCGGUGG GGGUUCACAC CUAUUUUUAA UAGGUGUGAA CCCCUCUUCG GGGUUCCGGU UCCCUUUCGG GUCCCGGAAC UUAAAUAAAA AUGGAAAGAA UUAAAUUAAU AUAAUGGUAU AACUGUGCGA UAAUUGUAAC ACAAACGAGU GAAACAAGUA CGUAAGUAUG GCAUAAUGAA CAAAUAACAC UGAUUGUAAA GGUUAUUGAU AACGAAUAAA AGUUACGCUA GGGAUAACAG GGUAAUAUAG CGAAAGAGUA GAUAUUGUAA GCUAUGUUUG CCACCUCGAU GUCGACUCAA CAUUUCCUCU UGGUUGUAAA AGCUAAGAAG GGUUUGACUG UUCGUCAAUU AAAAUGUUAC GUGAGUUGGG UUAAAUACGA UGUGAAUCAG UAUGGUUCCU AUCUGCUGAA GGAAAUAUUA UCAAAUUAAA UCUCAUUAUU AGUACGCAAG GACCAUAAUG AAUCAACCCA UGGUGUAUCU AUUGAUAAUA AUAUAAUAUA UUUAAUAAAA AUAAUACUUU AUUAAUAUAU UAUCUAUAUU AGUUUAUAUU UUAAUUAUAU AUUAUCAUAG UAGAUAAGCU AAGUUGAUAA UAAAUAAAUA UUGAAUACAU AUUAAAUAUG AAGUUGUUUU AAUAAGAUAA UUAAUCUGAU AAUUUUAUAC UAAAAUUAAU AAUUAUAGGU UUUAUAUAUU AUUUAUAAAU AAAUAUAUUA UAAUAAUAAU AAUUAUUAUU AUUAAUAAAA AAUAUUAAUU AUAAUAUUAA UAAAAUACUA AUUUAUCAGU UAUCUAUAUA AUAUCUAAUC UAUUAUUCUA UAUACU
MassTheoretical: 1.057789375 MDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: protein, uL2m

ProteinName: uL2m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.870023 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: protein, uL3m

ProteinName: uL3m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.528809 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, uL4m

ProteinName: uL4m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.254342 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, uL5m

ProteinName: uL5m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.014529 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, uL6m

ProteinName: uL6m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.690119 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, bL9m

ProteinName: bL9m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.763024 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, uL13m

ProteinName: uL13m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.125967 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, uL14m

ProteinName: uL14m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.929664 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, uL15m

ProteinName: uL15m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.765012 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, uL16m

ProteinName: uL16m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.347031 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, bL17m

ProteinName: bL17m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.858182 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, bL19m

ProteinName: bL19m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.179088 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, bL21m

ProteinName: bL21m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.507729 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, uL22m

ProteinName: uL22m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.964479 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, uL23m

ProteinName: uL23m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.529098 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, uL24m

ProteinName: uL24m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.67684 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, bL27m

ProteinName: bL27m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.516336 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, bL28m

ProteinName: bL28m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.193494 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, uL29m

ProteinName: uL29m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.410955 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, uL30m

ProteinName: uL30m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.088729 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, bL31m

ProteinName: bL31m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.125756 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, bL32m

ProteinName: bL32m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.409719 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, bL33m

ProteinName: bL33m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.275654 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: protein, bL34m

ProteinName: bL34m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.465526 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: protein, bL35m

ProteinName: bL35m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.206557 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: protein, bL36m

ProteinName: bL36m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.653594 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #29: protein, mL38

ProteinName: mL38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.703473 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #30: protein, mL40

ProteinName: mL40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.464595 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #31: protein, mL41

ProteinName: mL41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.841158 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #32: protein, mL43

ProteinName: mL43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.909393 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #33: protein, mL44

ProteinName: mL44 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.326758 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #34: protein, mL46

ProteinName: mL46 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.26174 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #35: protein, mL49

ProteinName: mL49 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.182286 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #36: protein, mL50

ProteinName: mL50 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.317365 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #37: protein, mL57

ProteinName: mL57 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.816342 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #38: protein, mL58

ProteinName: mL58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.507609 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #39: protein, mL59

ProteinName: mL59 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.408705 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #40: protein, mL60

ProteinName: mL60 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.277905 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #41: protein, mL67

ProteinName: mL67 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.712518 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #42: protein, bS1m

ProteinName: bS1m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.507457 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #43: protein, uS2m

ProteinName: uS2m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.585344 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #44: protein, uS3m

ProteinName: uS3m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.170996 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #45: protein, uS4m

ProteinName: uS4m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.450949 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #46: protein, uS5m

ProteinName: uS5m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.24009 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #47: protein, bS6m

ProteinName: bS6m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.310959 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #48: protein, uS7m

ProteinName: uS7m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.271279 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #49: protein, uS8m

ProteinName: uS8m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.365404 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #50: protein, uS9m

ProteinName: uS9m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.960496 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #51: protein, uS10m

ProteinName: uS10m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.395377 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #52: protein, uS11m

ProteinName: uS11m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.716566 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #53: protein, uS12m

ProteinName: uS12m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.5528 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #54: protein, uS13m

ProteinName: uS13m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.474945 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #55: protein, uS14m

ProteinName: uS14m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.563061 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #56: protein, uS15m

ProteinName: uS15m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.522064 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #57: protein, bS16m

ProteinName: bS16m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.402701 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #58: protein, uS17m

ProteinName: uS17m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.683986 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #59: protein, bS18m

ProteinName: bS18m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.447264 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #60: protein, uS19m

ProteinName: uS19m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.037476 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #61: protein, bS21m

ProteinName: bS21m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.872719 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #62: protein, mS23

ProteinName: mS23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.101824 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #63: protein, mS26

ProteinName: mS26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.737086 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #64: protein, mS29

ProteinName: mS29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.650645 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #65: protein, mS33

ProteinName: mS33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.030979 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #66: protein, mS35

ProteinName: mS35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.334529 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #67: protein, mS37

ProteinName: mS37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.305092 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #68: protein, mS38

ProteinName: mS38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.383451 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #69: protein, mS41

ProteinName: mS41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.796482 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #70: protein, mS42

ProteinName: mS42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.036896 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #71: protein, mS43

ProteinName: mS43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.775781 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #72: protein, mS44

ProteinName: mS44 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.045031 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #73: protein, mS45

ProteinName: mS45 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.763957 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #74: protein, mS46

ProteinName: mS46 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.897553 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #75: protein, mS47

ProteinName: mS47 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.367457 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #76: nucleic-acid, 15S ribosomal RNA

nucleic acidName: 15S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUAAAAAAUU UAUAAGAAUA UGAUGUUGGU UCAGAUUAAG CGCUAAAUAA GGACAUGACA CAUGCGAAUC AUACGUUUAU UAUUGAUAAG AUAAUAAAUA UGUGGUGUAA ACGUGAGUAA UUUUAUUAGG AAUUAAUGAA CUAUAGAAUA AGCUAAAUAC UUAAUAUAUU AUUAUAUAAA AAUAAUUUAU AUAAUAAAAA GGAUAUAUAU AUAAUAUAUA UUUAUCUAUA GUCAAGCCAA UAAUGGUUUA GGUAGUAGGU UUAUUAAGAG UUAAACCUAG CCAACGAUCC AUAAUCGAUA AUGAAAGUUA GAACGAUCAC GUUGACUCUG AAAUAUAGUC AAUAUCUAUA AGAUACAGCA GUGAGGAAUA UUGGACAAUG AUCGAAAGAU UGAUCCAGUU ACUUAUUAGG AUGAUAUAUA AAAAUAUUUU AUUUUAUUUA UAAAUAUUAA AUAUUUAUAA UAAUAAUAAU AAUAAUAUAU AUAUAUAAAU UGAUUAAAAA UAAAAUCCAU AAAUAAUUAA AAUAAUGAUA UUAAUUACCA UAUAUAUUUU UAUAUGGAUA UAUAUAUUAA UAAUAAUAUU AAUUUUAUUA UUAUUAAUAA UAUAUUUUAA UAGUCCUGAC UAAUAUUUGU GCCAGCAGUC GCGGUAACAC AAAGAGGGCG AGCGUUAAUC AUAAUGGUUU AAAGGAUCCG UAGAAUGAAU UAUAUAUUAU AAUUUAGAGU UAAUAAAAUA UAAUUAAAGA AUUAUAAUAG UAAAGAUGAA AUAAUAAUAA UAAUUAUAAG ACUAAUAUAU GUGAAAAUAU UAAUUAAAUA UUAACUGACA UUGAGGGAUU AAAACUAGAG UAGCGAAACG GAUUCGAUAC CCGUGUAGUU CUAGUAGUAA ACUAUGAAUA CAAUUAUUUA UAAUAUAUAU UAUAUAUAAA UAAUAAAUGA AAAUGAAAGU AUUCCACCUG AAGAGUACGU UAGCAAUAAU GAAACUCAAA ACAAUAGACG GUUACAGACU UAAGCAGUGG AGCAUGUUAU UUAAUUCGAU AAUCCACGAC UAACCUUACC AUAUUUUGAA UAUUAUAAUA AUUAUUAUAA UUAUUAUAUU ACAGGCGUUA CAUUGUUGUC UUUAGUUCGU GCUGCAAAGU UUUAGAUUAA GUUCAUAAAC GAACAAAACU CCAUAUAUAU AAUUUUAAUU AUAUAUAAUU UUAUAUUAUU UAUUAAUAUA AAGAAAGGAA UUAAGACAAA UCAUAAUGAU CCUUAUAAUA UGGGUAAUAG ACGUGCUAUA AUAAAAUGAU AAUAAAAUUA UAUAAAAUAU AUUUAAUUAU AUUUAAUUAA UAAUAUAAAA CAUUUUAAUU UUUAAUAUAU UUUUUUAUUA UAUAUUAAUA UGAAUUAUAA UCUGAAAUUC GAUUAUAUGA AAAAAGAAUU GCUAGUAAUA CGUAAAUUAG UAUGUUACGG UGAAUAUUCU AACUGUUUCG CACUAAUCAC UCAUCACGCG UUGAAACAUA UUAUUAUCUU AUUAUUUAUA UAAUAUUUUU UAAUAAAUAU UAAUAAUUAU UAAUUUAUAU UUAUUUAUAU CAGAAAUAAU AUGAAUUAAU GCGAAGUUGA AAUACAGUUA CCGUAGGGGA ACCUGCGGUG GGCUUAUAAA UAUCUUAAAU AUUCUUACA
MassTheoretical: 528.784125 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #77: nucleic-acid, tRNA

nucleic acidName: tRNATransfer RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCUACGUAG CUCAGUUGGU AGAGCACAUC ACUCAUAAUG AUGGGGUCAC AGGUUCGAAU CCCGUCGUAG CCACCA
MassTheoretical: 24.422523 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #78: protein, unknown protein sequence 1

ProteinName: unknown protein sequence 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.017875 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #79: protein, unknown protein sequence 2

ProteinName: unknown protein sequence 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.868854 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #80: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 299 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #81: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

+
Component #82: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #83: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 23.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Raw dataEMPIAR-10107 (Title: The Structure of the Yeast Mitochondrial Ribosome / Data size: 138.6
Data #1: Yeast mitochondrial ribosome - shiny particles [picked particles - multiframe - processed])

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 141795
3D reconstructionSoftware: RELION / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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