[English] 日本語
Yorodumi
- PDB-8d8j: Yeast mitochondrial small subunit assembly intermediate (State 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d8j
TitleYeast mitochondrial small subunit assembly intermediate (State 1)
Components
  • (37S ribosomal protein ...) x 11
  • 15S ribosomal RNA
  • Mitochondrial group I intron splicing factor CCM1
  • Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial
  • Protein FYV4, mitochondrial
  • uS12m
KeywordsRIBOSOME / Ribonucleoprotein complex Mitochondria Biogenesis
Function / homology
Function and homology information


mitochondrial small ribosomal subunit assembly / mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / RNA splicing / methyltransferase activity / mRNA processing / 4 iron, 4 sulfur cluster binding / ribosomal small subunit biogenesis / small ribosomal subunit ...mitochondrial small ribosomal subunit assembly / mitochondrial small ribosomal subunit / mitochondrial translation / sporulation resulting in formation of a cellular spore / RNA splicing / methyltransferase activity / mRNA processing / 4 iron, 4 sulfur cluster binding / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / translation / mitochondrion / RNA binding / metal ion binding
Similarity search - Function
Ribosomal protein S22, mitochondrial, budding yeast / Ribosomal protein Rsm22-like / Ribosomal protein S35, mitochondrial / : / Mitochondrial small ribosomal subunit Rsm22 / Eukaryotic mitochondrial regulator protein / PPR repeat family / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif ...Ribosomal protein S22, mitochondrial, budding yeast / Ribosomal protein Rsm22-like / Ribosomal protein S35, mitochondrial / : / Mitochondrial small ribosomal subunit Rsm22 / Eukaryotic mitochondrial regulator protein / PPR repeat family / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / IGR / Ribosomal protein S6/Translation elongation factor EF1B / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / 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 S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Tetratricopeptide-like helical domain superfamily / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal protein S12 signature. / RNA-binding S4 domain superfamily / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / MRPS12 isoform 1 / Mitochondrial 15S rRNA processing factor CCM1 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS26 ...IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / MRPS12 isoform 1 / Mitochondrial 15S rRNA processing factor CCM1 / 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 uS5m / Ribosome assembly protein RSM22, mitochondrial / Small ribosomal subunit protein mS41 / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS45 / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS8m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial
5: 37S ribosomal protein MRP13, mitochondrial
d: Mitochondrial group I intron splicing factor CCM1
O: 37S ribosomal protein S28, mitochondrial
P: 37S ribosomal protein S16, mitochondrial
Q: 37S ribosomal protein S17, mitochondrial
R: 37S ribosomal protein RSM18, mitochondrial
V: 37S ribosomal protein PET123, mitochondrial
2: Protein FYV4, mitochondrial
D: 37S ribosomal protein NAM9, mitochondrial
E: 37S ribosomal protein S5, mitochondrial
F: 37S ribosomal protein MRP17, mitochondrial
6: 37S ribosomal protein S35, mitochondrial
H: 37S ribosomal protein S8, mitochondrial
a: 15S ribosomal RNA
L: uS12m
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,085,44646
Polymers1,084,38916
Non-polymers1,05630
Water00
1


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

-
Components

-
Protein , 4 types, 4 molecules 0d2L

#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 Mitochondrial group I intron splicing factor CCM1


Mass: 101568.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4FBQ6
#9: 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
#16: 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: A0A6A5Q5F6

-
37S ribosomal protein ... , 11 types, 11 molecules 5OPQRVDEF6H

#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 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
#5: 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
#6: 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
#7: 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
#8: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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

-
RNA chain , 1 types, 1 molecules a

#15: 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

-
Non-polymers , 2 types, 30 molecules

#17: 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
#18: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Yeast mitochondrial small subunit assembly intermediate (State 3)
Type: RIBOSOME / Entity ID: #1-#16 / 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

-
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

-
Processing

EM software
IDNameVersionCategory
1crYOLO1.75particle selection
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: 3286640
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19720 / 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