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- PDB-8d8l: Yeast mitochondrial small subunit assembly intermediate (State 3) -

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Basic information

Entry
Database: PDB / ID: 8d8l
TitleYeast mitochondrial small subunit assembly intermediate (State 3)
Components
  • (37S ribosomal protein ...) x 28
  • 15S ribosomal RNA
  • 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
  • Mitochondrial 37S ribosomal protein S27
  • Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial
  • Protein FYV4, mitochondrial
  • Ribosomal protein VAR1, mitochondrial
  • unknown protein sequence
KeywordsRIBOSOME / Ribonucleoprotein complex Mitochondria Biogenesis
Function / homology
Function and homology information


Branched-chain amino acid catabolism / mitochondrial small ribosomal subunit assembly / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / valine catabolic process / Mitochondrial protein degradation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation ...Branched-chain amino acid catabolism / mitochondrial small ribosomal subunit assembly / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial translational initiation / valine catabolic process / Mitochondrial protein degradation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / superoxide dismutase activity / methyltransferase activity / peroxisome / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 4 iron, 4 sulfur cluster binding / small ribosomal subunit / small ribosomal subunit rRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTP binding / mitochondrion / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S22, mitochondrial, budding yeast / Helix Hairpins - #1480 / 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 ...Ribosomal protein S22, mitochondrial, budding yeast / Helix Hairpins - #1480 / 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 S35, mitochondrial / Ribosomal protein MRP10, mitochondrial / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Small ribosomal subunit protein mS41 SAM domain / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Ribosomal protein S6/Translation elongation factor EF1B / 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 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / CHCH / CHCH domain / Ribosomal Protein S5; domain 2 / 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. / Helicase, Ruva Protein; domain 3 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / 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 S2 signature 2. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S15 signature. / Ribosomal protein S4/S9
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS43 ...ADENOSINE-5'-TRIPHOSPHATE / IRON/SULFUR CLUSTER / : / 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 uS2m / Small ribosomal subunit protein uS5m / Ribosome assembly protein RSM22, mitochondrial / 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 / 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: 2.6 Å
AuthorsBurnside, C. / Harper, N. / Klinge, S.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM136640-02 United States
CitationJournal: Nature / Year: 2023
Title: Principles of mitoribosomal small subunit assembly in eukaryotes.
Authors: Nathan J Harper / Chloe Burnside / Sebastian Klinge /
Abstract: Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is ...Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism. Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.
History
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial
5: 37S ribosomal protein MRP13, mitochondrial
C: Ribosomal protein VAR1, 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
A: 37S ribosomal protein MRP51, mitochondrial
B: 37S ribosomal protein MRP4, mitochondrial
2: Protein FYV4, mitochondrial
3: 37S ribosomal protein S26, mitochondrial
D: 37S ribosomal protein NAM9, mitochondrial
4: 37S ribosomal protein MRP1, mitochondrial
E: 37S ribosomal protein S5, mitochondrial
F: 37S ribosomal protein MRP17, mitochondrial
6: 37S ribosomal protein S35, mitochondrial
G: 37S ribosomal protein S7, mitochondrial
H: 37S ribosomal protein S8, mitochondrial
8: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
I: 37S ribosomal protein S9, mitochondrial
a: 15S ribosomal RNA
J: 37S ribosomal protein S10, mitochondrial
K: 37S ribosomal protein S18, mitochondrial
c: unknown protein sequence
L: 37S ribosomal protein S12, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,558,108109
Polymers1,555,49935
Non-polymers2,60974
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules 0CX28c

#1: Protein Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial


Mass: 72308.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P36056, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Protein Ribosomal protein VAR1, mitochondrial / Mitochondrial small ribosomal subunit protein uS3m


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
#15: 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53305
#20: 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38783
#29: 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P28817, 3-hydroxyisobutyryl-CoA hydrolase
#34: Protein unknown protein sequence


Mass: 8017.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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37S ribosomal protein ... , 28 types, 28 molecules 5MNOPQRSTUVWYZAB3D4EF6GHIJKL

#2: Protein 37S ribosomal protein MRP13, mitochondrial / Mitochondrial small ribosomal subunit protein mS44 / YmS-A


Mass: 39045.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P12686
#4: Protein 37S ribosomal protein SWS2, mitochondrial / Mitochondrial small ribosomal subunit protein uS13m / Sick without securin protein 2


Mass: 16121.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53937
#5: Protein 37S ribosomal protein MRP2, mitochondrial / Mitochondrial small ribosomal subunit protein uS14m


Mass: 13563.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P10663
#6: Protein 37S ribosomal protein S28, mitochondrial / Mitochondrial small ribosomal subunit protein uS15m


Mass: 33116.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P21771
#7: Protein 37S ribosomal protein S16, mitochondrial / Mitochondrial small ribosomal subunit protein bS16m


Mass: 13663.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q02608
#8: Protein 37S ribosomal protein S17, mitochondrial / Mitochondrial small ribosomal subunit protein uS17m


Mass: 27683.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03246
#9: Protein 37S ribosomal protein RSM18, mitochondrial / Mitochondrial small ribosomal subunit protein bS18m


Mass: 15866.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40033
#10: Protein 37S ribosomal protein S19, mitochondrial / Mitochondrial small ribosomal subunit protein uS19m


Mass: 10292.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53733
#11: Protein 37S ribosomal protein MRP21, mitochondrial / Mitochondrial small ribosomal subunit protein bS21m


Mass: 20432.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38175
#12: Protein 37S ribosomal protein S25, mitochondrial / Mitochondrial small ribosomal subunit protein mS23


Mass: 30554.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40496
#13: Protein 37S ribosomal protein PET123, mitochondrial / Mitochondrial small ribosomal subunit protein mS26


Mass: 36059.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P17558
#14: Protein 37S ribosomal protein S23, mitochondrial / DAP-3 / Mitochondrial small ribosomal subunit protein mS29


Mass: 50940.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q01163
#16: Protein 37S ribosomal protein S24, mitochondrial / 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03976
#17: Protein 37S ribosomal protein MRP10, mitochondrial / Mitochondrial small ribosomal subunit protein mS37 / YmS-T


Mass: 10709.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O75012
#18: Protein 37S ribosomal protein MRP51, mitochondrial / Mitochondrial small ribosomal subunit protein bS1m


Mass: 39507.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q02950
#19: Protein 37S ribosomal protein MRP4, mitochondrial / Mitochondrial small ribosomal subunit protein uS2m


Mass: 44205.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32902
#21: Protein 37S ribosomal protein S26, mitochondrial / Mitochondrial small ribosomal subunit protein mS42


Mass: 30257.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P47141
#22: Protein 37S ribosomal protein NAM9, mitochondrial / 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P27929
#23: Protein 37S ribosomal protein MRP1, mitochondrial / Mitochondrial small ribosomal subunit protein mS43


Mass: 36775.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P10662
#24: Protein 37S ribosomal protein S5, mitochondrial / Mitochondrial small ribosomal subunit protein uS5m


Mass: 34941.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33759
#25: Protein 37S ribosomal protein MRP17, mitochondrial / Mitochondrial small ribosomal subunit protein bS6m / YmS16


Mass: 15046.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P28778
#26: Protein 37S ribosomal protein S35, mitochondrial / Mitochondrial small ribosomal subunit protein mS45


Mass: 39638.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53292
#27: Protein 37S ribosomal protein S7, mitochondrial / Mitochondrial small ribosomal subunit protein uS7m


Mass: 27857.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P47150
#28: Protein 37S ribosomal protein S8, mitochondrial / Mitochondrial small ribosomal subunit protein uS8m


Mass: 17496.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03799
#30: Protein 37S ribosomal protein S9, mitochondrial / Mitochondrial small ribosomal subunit protein uS9m


Mass: 31980.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38120
#32: Protein 37S ribosomal protein S10, mitochondrial / Mitochondrial small ribosomal subunit protein uS10m


Mass: 23458.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03201
#33: Protein 37S ribosomal protein S18, mitochondrial / Mitochondrial small ribosomal subunit protein uS11m / YmS18


Mass: 24603.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P42847
#35: Protein 37S ribosomal protein S12, mitochondrial / Mitochondrial small ribosomal subunit protein uS12m


Mass: 16948.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53732

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RNA chain , 1 types, 1 molecules a

#31: RNA chain 15S ribosomal RNA


Mass: 549234.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1887067169

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Non-polymers , 4 types, 77 molecules

#36: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical ChemComp-ATP / ADENOSINE-5'-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
#38: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#39: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Yeast mitochondrial small subunit assembly intermediate (State 3)
Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Molecular weightValue: 1.26 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELD / Calibrated magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 61.73 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14111

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.18CTF correction
7UCSF Chimeramodel fitting
8Coot0.9.5model fitting
10PHENIX1.19model refinement
11RELION3.1.1initial Euler assignment
12RELION3.1.1final Euler assignment
13RELION3.1.1classification
14PHENIX1.193D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3544843
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 381285
Details: 2 focused maps calculated in RELION 3.1.1 were combined into a composite map using phenix.combine_focused_maps. Composite half maps were generated by combining each half map from multi body refinements.
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5MRC

5mrc


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

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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

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