[English] 日本語
Yorodumi
- PDB-8om3: Small subunit of yeast mitochondrial ribosome in complex with IF3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8om3
TitleSmall subunit of yeast mitochondrial ribosome in complex with IF3/Aim23.
Components
  • (37S ribosomal protein ...) x 28
  • (Mitochondrial ...Mitochondrion) x 2
  • 15S mitochondrial rRNA
  • 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
  • Altered inheritance of mitochondria protein 23, mitochondrial
  • Protein FYV4, mitochondrial
  • Ribosomal protein VAR1, mitochondrialRibosome
KeywordsRIBOSOME / mitochondria / initiation factor 3 / pre-initiation complex
Function / homology
Function and homology information


Branched-chain amino acid catabolism / 3-hydroxyisobutyryl-CoA hydrolase / mitochondrial translational initiation / 3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / mitochondrial ribosome binding / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / sporulation resulting in formation of a cellular spore ...Branched-chain amino acid catabolism / 3-hydroxyisobutyryl-CoA hydrolase / mitochondrial translational initiation / 3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / mitochondrial ribosome binding / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / translation initiation factor activity / mRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTP binding / mitochondrion / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Altered inheritance of mitochondria protein 23, mitochondrial / Mitochondrial translation initiation factor / Ribosomal protein VAR1 / : / Mitochondrial ribosomal protein (VAR1) / Mitochondrial ribosomal protein MRP51, fungi / Mitochondrial ribosomal protein S25 / Ribosomal protein S24, mitochondrial / Ribosomal protein S23, mitochondrial, fungi / Mitochondrial ribosomal protein subunit ...Altered inheritance of mitochondria protein 23, mitochondrial / Mitochondrial translation initiation factor / Ribosomal protein VAR1 / : / Mitochondrial ribosomal protein (VAR1) / 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 / IGR protein motif / IGR / 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 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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 / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / ClpP/crotonase-like domain superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S14, conserved site / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S14 / Ribosomal protein S2 / Ribosomal protein S4, conserved site / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / RNA-binding S4 domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS43 / Small ribosomal subunit protein uS14m ...ADENOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein uS4m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS47 / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein uS5m / 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 / Small ribosomal subunit protein uS11m / Altered inheritance of mitochondria protein 23, mitochondrial / Small ribosomal subunit protein mS42 / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein mS45 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS19m / Small ribosomal subunit protein uS13m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS8m / Small ribosomal subunit protein mS35
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsItoh, Y. / Chicherin, I. / Kamenski, P. / Amunts, A.
Funding supportEuropean Union, Sweden, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
CitationJournal: Mol Cell / Year: 2024
Title: METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.
Authors: Tslil Ast / Yuzuru Itoh / Shayan Sadre / Jason G McCoy / Gil Namkoong / Jordan C Wengrod / Ivan Chicherin / Pallavi R Joshi / Piotr Kamenski / Daniel L M Suess / Alexey Amunts / Vamsi K Mootha /
Abstract: Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular ...Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [FeS] cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 37S ribosomal protein MRP51, mitochondrial
B: 37S ribosomal protein MRP4, mitochondrial
C: Ribosomal protein VAR1, mitochondrial
D: 37S ribosomal protein NAM9, mitochondrial
E: 37S ribosomal protein S5, mitochondrial
F: 37S ribosomal protein MRP17, mitochondrial
G: 37S ribosomal protein S7, mitochondrial
H: 37S ribosomal protein S8, mitochondrial
I: 37S ribosomal protein S9, mitochondrial
J: 37S ribosomal protein S10, mitochondrial
K: 37S ribosomal protein S18, mitochondrial
L: 37S ribosomal protein S12, mitochondrial
M: 37S ribosomal protein SWS2, mitochondrial
N: 37S ribosomal protein MRP2, mitochondrial
O: 37S ribosomal protein S28, mitochondrial
P: 37S ribosomal protein S16, mitochondrial
Q: 37S ribosomal protein S17, mitochondrial
R: 37S ribosomal protein RSM18, mitochondrial
S: 37S ribosomal protein S19, mitochondrial
T: 37S ribosomal protein MRP21, mitochondrial
U: 37S ribosomal protein S25, mitochondrial
V: 37S ribosomal protein PET123, mitochondrial
W: 37S ribosomal protein S23, mitochondrial
X: Mitochondrial 37S ribosomal protein S27
Y: 37S ribosomal protein S24, mitochondrial
Z: 37S ribosomal protein MRP10, mitochondrial
1: Mitochondrial mRNA-processing protein COX24
2: Protein FYV4, mitochondrial
3: 37S ribosomal protein S26, mitochondrial
4: 37S ribosomal protein MRP1, mitochondrial
5: 37S ribosomal protein MRP13, mitochondrial
6: 37S ribosomal protein S35, mitochondrial
8: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
r: 15S mitochondrial rRNA
d: Altered inheritance of mitochondria protein 23, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,513,707159
Polymers1,509,34035
Non-polymers4,368124
Water26,7341484
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
37S ribosomal protein ... , 28 types, 28 molecules ABDEFGHIJKLMNOPQRSTUVWYZ3456

#1: Protein 37S ribosomal protein MRP51, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein bS1m


Mass: 39507.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q02950
#2: Protein 37S ribosomal protein MRP4, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS2m


Mass: 44205.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P32902
#4: Protein 37S ribosomal protein NAM9, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS4m / Nuclear accommodation of mitochondria protein 9


Mass: 56450.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P27929
#5: Protein 37S ribosomal protein S5, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS5m


Mass: 34941.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P33759
#6: Protein 37S ribosomal protein MRP17, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein bS6m / YmS16


Mass: 15046.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P28778
#7: Protein 37S ribosomal protein S7, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS7m


Mass: 27857.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P47150
#8: Protein 37S ribosomal protein S8, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS8m


Mass: 17391.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q03799
#9: Protein 37S ribosomal protein S9, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS9m


Mass: 31980.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P38120
#10: Protein 37S ribosomal protein S10, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS10m


Mass: 23458.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q03201
#11: Protein 37S ribosomal protein S18, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS11m / YmS18


Mass: 24603.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P42847
#12: Protein 37S ribosomal protein S12, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS12m


Mass: 16948.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P53732
#13: Protein 37S ribosomal protein SWS2, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS13m / Sick without securin protein 2


Mass: 16087.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P53937
#14: Protein 37S ribosomal protein MRP2, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS14m


Mass: 13563.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P10663
#15: Protein 37S ribosomal protein S28, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS15m


Mass: 33116.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P21771
#16: Protein 37S ribosomal protein S16, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein bS16m


Mass: 13663.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q02608
#17: Protein 37S ribosomal protein S17, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS17m


Mass: 27683.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q03246
#18: Protein 37S ribosomal protein RSM18, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein bS18m


Mass: 15866.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P40033
#19: Protein 37S ribosomal protein S19, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS19m


Mass: 10292.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P53733
#20: Protein 37S ribosomal protein MRP21, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein bS21m


Mass: 20432.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P38175
#21: Protein 37S ribosomal protein S25, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS23


Mass: 30554.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P40496
#22: Protein 37S ribosomal protein PET123, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS26


Mass: 36059.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P17558
#23: Protein 37S ribosomal protein S23, mitochondrial / Ribosome / DAP-3 / Mitochondrial small ribosomal subunit protein mS29


Mass: 50940.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q01163
#25: Protein 37S ribosomal protein S24, mitochondrial / Ribosome / Mitochondrial ribosomal small subunit protein 24 / Mitochondrial small ribosomal subunit protein mS35


Mass: 37458.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: Q03976
#26: Protein 37S ribosomal protein MRP10, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS37 / YmS-T


Mass: 10709.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O75012
#29: Protein 37S ribosomal protein S26, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS42


Mass: 30257.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47141
#30: Protein 37S ribosomal protein MRP1, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS43


Mass: 36775.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P10662
#31: Protein 37S ribosomal protein MRP13, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS44 / YmS-A


Mass: 39045.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P12686
#32: Protein 37S ribosomal protein S35, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein mS45


Mass: 39638.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P53292

-
Protein , 4 types, 4 molecules C28d

#3: Protein Ribosomal protein VAR1, mitochondrial / Ribosome / Mitochondrial small ribosomal subunit protein uS3m


Mass: 47170.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P02381
#28: Protein Protein FYV4, mitochondrial / Function required for yeast viability protein 4 / Mitochondrial small ribosomal subunit protein mS41


Mass: 15321.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P38783
#33: Protein 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial / / 3-hydroxyisobutyryl-coenzyme A hydrolase / HIB-CoA hydrolase / HIBYL-CoA-H / Mitochondrial small ...3-hydroxyisobutyryl-coenzyme A hydrolase / HIB-CoA hydrolase / HIBYL-CoA-H / Mitochondrial small ribosomal subunit protein mS47


Mass: 56351.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a
References: UniProt: P28817, 3-hydroxyisobutyryl-CoA hydrolase
#35: Protein Altered inheritance of mitochondria protein 23, mitochondrial


Mass: 42613.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: XPM171a / Gene: AIM23, YJL131C, J0682 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P47015

-
Mitochondrial ... , 2 types, 2 molecules X1

#24: Protein Mitochondrial 37S ribosomal protein S27 / Mitochondrial small ribosomal subunit protein mS33


Mass: 12420.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P53305
#27: Protein Mitochondrial mRNA-processing protein COX24 / Mitochondrial small ribosomal subunit protein mS38


Mass: 12800.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a / References: UniProt: P32344

-
RNA chain / Sugars , 2 types, 2 molecules r

#34: RNA chain 15S mitochondrial rRNA


Mass: 528125.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: XPM171a
#38: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 1607 molecules

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


Mass: 24.305 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: Mg
#37: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: K
#39: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#40: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1484 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Small subunit of mitochondrial ribosome in complex with IF3/Aim23
Type: RIBOSOME / Entity ID: #1-#7, #9-#35 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMpotassium chlorideKCl1
220 mMHEPES-KOH buffer pH7.51
35.0 mMmagnesium acetate1
42.0 mMdithiothreitol1
50.05 %n-dodecyl-beta-D-maltoside1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 / Nominal magnification: 165000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 40 eV

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7Coot0.9model fitting
9RELION3initial Euler assignment
10RELION3.1final Euler assignment
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53922 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5MRC

5mrc


Accession code: 5MRC / Source name: PDB / Type: experimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more