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- PDB-5mrf: Structure of the yeast mitochondrial ribosome - Class C -

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Basic information

Entry
Database: PDB / ID: 5mrf
TitleStructure of the yeast mitochondrial ribosome - Class C
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 / saccharomyces cerevisiae
Function / homology
Function and homology information


Branched-chain amino acid catabolism / 3-hydroxyisobutyryl-CoA hydrolase / positive regulation of mitochondrial DNA replication / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / valine catabolic process / DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / mitochondrial large ribosomal subunit ...Branched-chain amino acid catabolism / 3-hydroxyisobutyryl-CoA hydrolase / positive regulation of mitochondrial DNA replication / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / valine catabolic process / DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / RNA processing / cell redox homeostasis / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / mRNA processing / rRNA processing / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / double-stranded RNA binding / single-stranded DNA binding / ribosome biogenesis / large ribosomal subunit / cellular response to oxidative stress / small ribosomal subunit / cytosolic large ribosomal subunit / transferase activity / DNA recombination / mitochondrial inner membrane / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTP binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / Ribosomal protein VAR1 / : / : / Mitochondrial ribosomal protein (VAR1) / Mitochondrial ribosomal protein subunit L20 / Ribosomal protein L31p, N-terminal ...54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / Ribosomal protein VAR1 / : / : / Mitochondrial ribosomal protein (VAR1) / Mitochondrial ribosomal protein subunit L20 / Ribosomal protein L31p, N-terminal / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L3, double-stranded RNA binding domain / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / 54S ribosomal protein L28, mitochondrial / Ribosomal protein L31, mitochondrial / 54S ribosomal protein L36, yeast / Mitochondrial ribosomal protein L31 / Mitochondrial ribosomal protein MRP51, fungi / Mitochondrial ribosomal protein S25 / Ribosomal protein S24, mitochondrial / Ribosomal protein S23, mitochondrial, fungi / Mitochondrial ribosomal protein subunit / Mitochondrial ribosomal protein S25 / Ribosomal protein MRP10, mitochondrial / Ribosomal protein S35, mitochondrial / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase domain / IGR protein motif / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / Ribonuclease-III-like / IGR protein motif / IGR / Ribonuclease III / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Ribosomal protein L49/IMG2 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial large subunit ribosomal protein (Img2) / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Enoyl-CoA hydratase/isomerase, conserved site / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Enoyl-CoA hydratase/isomerase signature. / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS43 / Small ribosomal subunit protein uS14m ...GUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36m / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS43 / Small ribosomal subunit protein uS14m / Small ribosomal subunit protein mS27 / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL60 / Small ribosomal subunit protein mS26 / Large ribosomal subunit protein uL30m / Small ribosomal subunit protein uS15m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein mL59 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein mL49 / Small ribosomal subunit protein uS4m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS47 / Large ribosomal subunit protein uL3m / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL2m / Small ribosomal subunit protein uS2m / Large ribosomal subunit protein uL6m / Small ribosomal subunit protein uS5m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL5m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein mL57 / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein bL31m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS41 / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Large ribosomal subunit protein bL21m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein mS42 / Small ribosomal subunit protein uS7m / Large ribosomal subunit protein uL4m / Small ribosomal subunit protein mS45 / Small ribosomal subunit protein mS33 / Large ribosomal subunit protein bL9m / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS19m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL35m / Small ribosomal subunit protein uS13m / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein mL50 / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein mS46 / Small ribosomal subunit protein uS8m / Small ribosomal subunit protein mS35 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL67 / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL13m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.97 Å
AuthorsDesai, N. / Brown, A. / Amunts, A. / Ramakrishnan, V.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome TrustWT096570 United Kingdom
Wellcome Trust110301/Z/15/Z United Kingdom
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Agouron Institute United Kingdom
Louis-Jeantet Foundation United Kingdom
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.
History
DepositionDec 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Derived calculations / Category: em_image_scans / pdbx_struct_conn_angle
Revision 1.2Feb 7, 2018Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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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
Polymers3,317,72278
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 method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#75: RNA chain 15S ribosomal RNA /


Mass: 528784.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#76: RNA chain tRNA / Transfer RNA


Mass: 24422.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Protein , 70 types, 70 molecules BCDEFGHIJKLMNOPQRSTUVWXZ123456...

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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 7275.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36533
#26: Protein bL35m / Putative mitochondrial ribosomal protein YNL122C


Mass: 7206.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53921
#28: Protein mL38 / 54S ribosomal protein L35 / mitochondrial / YmL35


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 29585.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32902
#43: Protein uS3m / Ribosomal protein VAR1 / mitochondrial


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 10305.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O75012
#68: Protein mS41 / Protein FYV4 / mitochondrial / Function required for yeast viability protein 4


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


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


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


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


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


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


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

-
Protein/peptide , 3 types, 3 molecules Y011

#25: Protein/peptide bL34m / 54S ribosomal protein L34 / mitochondrial / L34mt


Mass: 5465.526 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04598
#27: Protein/peptide bL36m / 54S ribosomal protein RTC6 / mitochondrial / Restriction of telomere capping protein 6 / ...54S ribosomal protein RTC6 / mitochondrial / Restriction of telomere capping protein 6 / Translation associated element 4


Mass: 4653.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O14464
#67: Protein/peptide mS38 / Mitochondrial mRNA-processing protein COX24


Mass: 4383.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32344

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

#77: Protein unknown protein sequence 1


Mass: 8017.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#78: Protein unknown protein sequence 2


Mass: 12868.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
Non-polymers , 4 types, 303 molecules

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


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


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#82: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: yeast mitochondrial ribosome - class C / Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: 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)

-
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: 4.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24632 / Symmetry type: POINT

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