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- PDB-5mre: Structure of the yeast mitochondrial ribosome - Class B -

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Entry
Database: PDB / ID: 5mre
TitleStructure of the yeast mitochondrial ribosome - Class B
Components
  • (unknown protein sequence ...) x 2
  • 15S ribosomal RNA
  • 21S ribosomal RNA
  • bL17m
  • bL19m
  • bL21m
  • bL27m
  • bL28m
  • bL31m
  • bL32m
  • bL33m
  • bL34m
  • bL35m
  • bL36m
  • bL9m
  • bS16m
  • bS18m
  • bS1m
  • bS21m
  • bS6m
  • mL38
  • mL40
  • mL41
  • mL43
  • mL44
  • mL46
  • mL49
  • mL50
  • mL57
  • mL58
  • mL59
  • mL60
  • mL67
  • mS23
  • mS26
  • mS29
  • mS33
  • mS35
  • mS37
  • mS38
  • mS41
  • mS42
  • mS43
  • mS44
  • mS45
  • mS46
  • mS47
  • tRNATransfer RNA
  • uL13m
  • uL14m
  • uL15m
  • uL16m
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL2m
  • uL30m
  • uL3m
  • uL4m
  • uL5m
  • uL6m
  • uS10m
  • uS11m
  • uS12m
  • uS13m
  • uS14m
  • uS15m
  • uS17m
  • uS19m
  • uS2m
  • uS3m
  • uS4m
  • uS5m
  • uS7m
  • uS8m
  • uS9m
KeywordsRIBOSOME / yeast / mitochondrial / ribosome / saccharomyces cerevisiae
Function / homologyMitochondrial ribosomal protein mL59 / RNA-binding S4 domain superfamily / Protein Fyv4 / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / MRP-L47 superfamily, mitochondrial / 54S ribosomal protein L25 / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein S11 superfamily ...Mitochondrial ribosomal protein mL59 / RNA-binding S4 domain superfamily / Protein Fyv4 / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / MRP-L47 superfamily, mitochondrial / 54S ribosomal protein L25 / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein S11 superfamily / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S24/S35, mitochondrial / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein L16p/L10e / 54S ribosomal protein L15, mitochondrial / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Double-stranded RNA binding motif / 54S ribosomal protein L35, mitochondrial / Ribosomal protein S7 domain superfamily / ACP-like superfamily / Ribosomal protein L6 / Ribosomal protein S19, superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L28/L24 / Mitochondrial homologous recombination protein 1 / Ribosomal protein L20, mitochondrial / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein S10 domain / Ribosomal protein L13, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L46, N-terminal / Ribosomal protein L35 / 30s ribosomal protein S13, C-terminal / Ribosomal protein L21-like / PEBP-like superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L22/L17 superfamily / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L17 superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Thioredoxin-like superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein S6 superfamily / ClpP/crotonase-like domain superfamily / Ribosomal protein L36 superfamily / Phosphatidylethanolamine-binding protein, eukaryotic / L28p-like / 54S ribosomal protein L36, yeast / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein S10p/S20e / Ribosomal protein S17 / Ribosomal protein S35, mitochondrial / Ribosomal protein S9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein S5 signature. / Ribosomal protein S14 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L3 signature. / Ribosomal protein L2 signature. / Ribosomal protein S15 signature. / Ribosomal protein S19 signature. / Ribosomal protein L30 signature. / Enoyl-CoA hydratase/isomerase signature. / Ribosomal protein S12 signature. / Ribosomal protein S7 signature. / Ribosomal protein L14 signature. / Enoyl-CoA hydratase/isomerase / Ribonuclease-III-like
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.75 Å resolution
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 Report
SummaryFull reportAbout validation report
DateDeposition: Dec 22, 2016 / Release: Feb 15, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 15, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Derived calculationsem_image_scans / pdbx_struct_conn_angle
1.2Feb 7, 2018Structure modelStructure summaryentity_entity.pdbx_description
1.3Nov 21, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 21S ribosomal RNA
B: uL2m
C: uL3m
D: uL4m
E: uL5m
F: uL6m
G: bL9m
H: uL13m
I: uL14m
J: uL15m
K: uL16m
L: bL17m
M: bL19m
N: bL21m
O: uL22m
P: uL23m
Q: uL24m
R: bL27m
S: bL28m
T: uL29m
U: uL30m
V: bL31m
W: bL32m
X: bL33m
Y: bL34m
Z: bL35m
0: bL36m
1: mL38
2: mL40
3: mL41
4: mL43
5: mL44
6: mL46
7: mL49
8: mL50
9: mL57
a: mL58
b: mL59
c: mL60
d: mL67
AA: bS1m
BB: uS2m
CC: uS3m
DD: uS4m
EE: uS5m
FF: bS6m
GG: uS7m
HH: uS8m
II: uS9m
JJ: uS10m
KK: uS11m
LL: uS12m
MM: uS13m
NN: uS14m
OO: uS15m
PP: bS16m
QQ: uS17m
RR: bS18m
SS: uS19m
TT: bS21m
UU: mS23
VV: mS26
WW: mS29
XX: mS33
YY: mS35
ZZ: mS37
11: mS38
22: mS41
33: mS42
44: mS43
55: mS44
66: mS45
77: mS46
88: mS47
aa: 15S ribosomal RNA
bb: tRNA
cc: unknown protein sequence 1
dd: unknown protein sequence 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,325,586381
Polyers3,317,72278
Non-polymers7,864303
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules Aaabb

#1: RNA chain 21S ribosomal RNA /


Mass: 1057789.375 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#75: RNA chain 15S ribosomal RNA /


Mass: 528784.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#76: RNA chain tRNA / Transfer RNA


Mass: 24422.523 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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Protein/peptide , 73 types, 73 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01234...

#2: Protein/peptide uL2m / 54S ribosomal protein RML2 / mitochondrial / L2


Mass: 43870.023 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32611
#3: Protein/peptide uL3m / 54S ribosomal protein L9 / mitochondrial / YmL9


Mass: 27528.809 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P31334
#4: Protein/peptide uL4m / 54S ribosomal protein YmL6 / mitochondrial


Mass: 28254.342 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P51998
#5: Protein/peptide uL5m / 54S ribosomal protein L7 / mitochondrial / YmL5 / YmL7


Mass: 31014.529 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36519
#6: Protein/peptide uL6m / 54S ribosomal protein L6 / mitochondrial / YmL16


Mass: 21690.119 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32904
#7: Protein/peptide bL9m / 54S ribosomal protein L50 / mitochondrial


Mass: 8763.024 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53724
#8: Protein/peptide uL13m / 54S ribosomal protein L23 / mitochondrial / YmL23


Mass: 18125.967 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12487
#9: Protein/peptide uL14m / 54S ribosomal protein L38 / mitochondrial / YmL38


Mass: 14929.664 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35996
#10: Protein/peptide uL15m / 54S ribosomal protein L10 / mitochondrial / YmL10/YmL18


Mass: 24765.012 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36520
#11: Protein/peptide uL16m / 54S ribosomal protein L16 / mitochondrial / YmL47


Mass: 22347.031 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38064
#12: Protein/peptide bL17m / 54S ribosomal protein L8 / mitochondrial / YmL8


Mass: 26858.182 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22353
#13: Protein/peptide bL19m / 54S ribosomal protein IMG1 / mitochondrial / Integrity of mitochondrial genome protein 1 / PetCR46


Mass: 17179.088 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25626
#14: Protein/peptide bL21m / 54S ribosomal protein L49 / mitochondrial / YmL49


Mass: 13507.729 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40858
#15: Protein/peptide uL22m / 54S ribosomal protein L22 / mitochondrial


Mass: 25964.479 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53881
#16: Protein/peptide uL23m / 54S ribosomal protein L41 / mitochondrial / YmL41


Mass: 24529.098 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32387
#17: Protein/peptide uL24m / 54S ribosomal protein L40 / mitochondrial / YmL40


Mass: 33676.840 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36534
#18: Protein/peptide bL27m / 54S ribosomal protein L2 / mitochondrial / YMR6 / YmL2


Mass: 39516.336 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P12687
#19: Protein/peptide bL28m / 54S ribosomal protein L24 / mitochondrial / YmL14/YmL24


Mass: 25193.494 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36525
#20: Protein/peptide uL29m / 54S ribosomal protein L4 / mitochondrial / YmL4


Mass: 26410.955 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36517
#21: Protein/peptide uL30m / 54S ribosomal protein L33 / mitochondrial / YmL33


Mass: 9088.729 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20084
#22: Protein/peptide bL31m / 54S ribosomal protein L36 / mitochondrial / YmL36


Mass: 20125.756 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36531
#23: Protein/peptide bL32m / 54S ribosomal protein L32 / mitochondrial / YmL32


Mass: 13409.719 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25348
#24: Protein/peptide bL33m / 54S ribosomal protein L39 / mitochondrial / YmL39


Mass: 7275.654 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36533
#25: Protein/peptide bL34m / 54S ribosomal protein L34 / mitochondrial / L34mt


Mass: 5465.526 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q04598
#26: Protein/peptide bL35m / Putative mitochondrial ribosomal protein YNL122C


Mass: 7206.557 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53921
#27: Protein/peptide bL36m / 54S ribosomal protein RTC6 / mitochondrial / Restriction of telomere capping protein 6 / Translation associated element 4


Mass: 4653.594 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: O14464
#28: Protein/peptide mL38 / 54S ribosomal protein L35 / mitochondrial / YmL35


Mass: 40703.473 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q06678
#29: Protein/peptide mL40 / 54S ribosomal protein L28 / mitochondrial / YmL28


Mass: 13464.595 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36527
#30: Protein/peptide mL41 / 54S ribosomal protein L27 / mitochondrial / YmL27


Mass: 14841.158 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36526
#31: Protein/peptide mL43 / 54S ribosomal protein L51 / mitochondrial


Mass: 15909.393 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q06090
#32: Protein/peptide mL44 / 54S ribosomal protein L3 / mitochondrial / YmL3


Mass: 36326.758 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36516
#33: Protein/peptide mL46 / 54S ribosomal protein L17 / mitochondrial / YmL17/YmL30


Mass: 32261.740 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36528
#34: Protein/peptide mL49 / 54S ribosomal protein IMG2 / mitochondrial / Integrity of mitochondrial genome protein 2


Mass: 12182.286 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25642
#35: Protein/peptide mL50 / 54S ribosomal protein L13 / mitochondrial / YmL13


Mass: 30317.365 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02204
#36: Protein/peptide mL57 / 54S ribosomal protein L15 / mitochondrial / YmL15


Mass: 23816.342 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36523
#37: Protein/peptide mL58 / 54S ribosomal protein L20 / mitochondrial / YmL20


Mass: 20507.609 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22354
#38: Protein/peptide mL59 / 54S ribosomal protein L25 / mitochondrial / YmL25


Mass: 18408.705 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P23369
#39: Protein/peptide mL60 / 54S ribosomal protein L31 / mitochondrial / YmL31


Mass: 14277.905 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14063
#40: Protein/peptide mL67 / Mitochondrial homologous recombination protein 1 / Cross-linked transcription component 1


Mass: 25712.518 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q06630
#41: Protein/peptide bS1m / 37S ribosomal protein MRP51 / mitochondrial


Mass: 39507.457 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02950
#42: Protein/peptide uS2m / 37S ribosomal protein MRP4 / mitochondrial


Mass: 29585.344 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32902
#43: Protein/peptide uS3m / Ribosomal protein VAR1 / mitochondrial


Mass: 47170.996 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02381
#44: Protein/peptide uS4m / 37S ribosomal protein NAM9 / mitochondrial / Nuclear accommodation of mitochondria protein 9


Mass: 56450.949 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P27929
#45: Protein/peptide uS5m / 37S ribosomal protein S5 / mitochondrial


Mass: 33240.090 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P33759
#46: Protein/peptide bS6m / 37S ribosomal protein MRP17 / mitochondrial / YmS16


Mass: 14310.959 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P28778
#47: Protein/peptide uS7m / 37S ribosomal protein S7 / mitochondrial


Mass: 18271.279 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P47150
#48: Protein/peptide uS8m / 37S ribosomal protein S8 / mitochondrial


Mass: 17365.404 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03799
#49: Protein/peptide uS9m / 37S ribosomal protein S9 / mitochondrial


Mass: 27960.496 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38120
#50: Protein/peptide uS10m / 37S ribosomal protein S10 / mitochondrial


Mass: 21395.377 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03201
#51: Protein/peptide uS11m / 37S ribosomal protein S18 / mitochondrial / YmS18


Mass: 16716.566 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P42847
#52: Protein/peptide uS12m / 37S ribosomal protein S12 / mitochondrial


Mass: 13552.800 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53732
#53: Protein/peptide uS13m / 37S ribosomal protein SWS2 / mitochondrial / Sick without securin protein 2


Mass: 13474.945 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53937
#54: Protein/peptide uS14m / 37S ribosomal protein MRP2 / mitochondrial


Mass: 13563.061 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10663
#55: Protein/peptide uS15m / 37S ribosomal protein S28 / mitochondrial


Mass: 29522.064 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P21771
#56: Protein/peptide bS16m / 37S ribosomal protein S16 / mitochondrial


Mass: 13402.701 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02608
#57: Protein/peptide uS17m / 37S ribosomal protein S17 / mitochondrial


Mass: 27683.986 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03246
#58: Protein/peptide bS18m / 37S ribosomal protein RSM18 / mitochondrial


Mass: 11447.264 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40033
#59: Protein/peptide uS19m / 37S ribosomal protein S19 / mitochondrial


Mass: 9037.476 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53733
#60: Protein/peptide bS21m / 37S ribosomal protein MRP21 / mitochondrial


Mass: 10872.719 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38175
#61: Protein/peptide mS23 / 37S ribosomal protein S25 / mitochondrial


Mass: 27101.824 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40496
#62: Protein/peptide mS26 / 37S ribosomal protein PET123 / mitochondrial


Mass: 26737.086 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17558
#63: Protein/peptide mS29 / 37S ribosomal protein S23 / mitochondrial / DAP-3


Mass: 45650.645 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q01163
#64: Protein/peptide mS33 / Mitochondrial 37S ribosomal protein S27


Mass: 11030.979 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53305
#65: Protein/peptide mS35 / 37S ribosomal protein S24 / mitochondrial / Mitochondrial ribosomal small subunit protein 24


Mass: 32334.529 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03976
#66: Protein/peptide mS37 / 37S ribosomal protein MRP10 / mitochondrial / YmS-T


Mass: 10305.092 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: O75012
#67: Protein/peptide mS38 / Mitochondrial mRNA-processing protein COX24


Mass: 4383.451 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32344
#68: Protein/peptide mS41 / Protein FYV4 / mitochondrial / Function required for yeast viability protein 4


Mass: 11796.482 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38783
#69: Protein/peptide mS42 / 37S ribosomal protein S26 / mitochondrial


Mass: 29036.896 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P47141
#70: Protein/peptide mS43 / 37S ribosomal protein MRP1 / mitochondrial


Mass: 36775.781 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10662
#71: Protein/peptide mS44 / 37S ribosomal protein MRP13 / mitochondrial / YmS-A


Mass: 39045.031 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P12686
#72: Protein/peptide mS45 / 37S ribosomal protein S35 / mitochondrial


Mass: 36763.957 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53292
#73: Protein/peptide mS46 / 37S ribosomal protein RSM28 / mitochondrial


Mass: 18897.553 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03430
#74: Protein/peptide mS47 / 3-hydroxyisobutyryl-CoA hydrolase / mitochondrial / 3-hydroxyisobutyryl-coenzyme A hydrolase / HIBYL-CoA-H


Mass: 51367.457 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
References: UniProt: P28817, 3-hydroxyisobutyryl-CoA hydrolase

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Unknown protein sequence ... , 2 types, 2 molecules ccdd

#77: Protein/peptide unknown protein sequence 1


Mass: 8017.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#78: Protein/peptide unknown protein sequence 2


Mass: 12868.854 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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Non-polymers , 4 types, 303 molecules

#79: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 299 / Formula: Mg / Magnesium
#80: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#81: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#82: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: yeast mitochondrial ribosome - Class B / Type: RIBOSOME
Entity ID: 1, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 23.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4RELION1.4CTF correction
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 55448 / Symmetry type: POINT

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