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- EMDB-5941: Cryo-EM structure of the small subunit of the mammalian mitochond... -

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Basic information

Entry
Database: EMDB / ID: EMD-5941
TitleCryo-EM structure of the small subunit of the mammalian mitochondrial ribosome
Map datamammalian mito-ribosome small subunit structure
Sample
  • Sample: small subunit of mito-ribosome
  • Complex: mito-ribosomal small subunit
Keywordsmammalian mito-ribosome small subunit structure
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / peptide biosynthetic process / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / Mitochondrial protein degradation ...Mitochondrial translation elongation / Mitochondrial translation termination / peptide biosynthetic process / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / Mitochondrial protein degradation / ribosomal small subunit binding / small ribosomal subunit rRNA binding / kinase activity / regulation of translation / ribosomal small subunit assembly / cell population proliferation / tRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / apoptotic process / mitochondrion / RNA binding / nucleoplasm
Similarity search - Function
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial ...Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / : / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / 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 / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 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 / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 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 S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / 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 S5, C-terminal domain / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S9 / Ribosomal protein S9/S16
Similarity search - Domain/homology
Small ribosomal subunit protein uS15m / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS40 ...Small ribosomal subunit protein uS15m / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS40 / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein uS12m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein uS14m
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsKaushal PS / Sharma MR / Booth TM / Haque E / Tung C / Sanbonmatsu K / Spremulli L / Agrawal RK
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome.
Authors: Prem S Kaushal / Manjuli R Sharma / Timothy M Booth / Emdadul M Haque / Chang-Shung Tung / Karissa Y Sanbonmatsu / Linda L Spremulli / Rajendra K Agrawal /
Abstract: The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ...The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. Here we present the cryo-EM structure analysis of the small (28S) subunit (SSU) of the 55S mitoribosome. We find that the mito-specific extensions in homologous MRPs generally are involved in inter-MRP contacts and in contacts with mito-specific MRPs, suggesting a stepwise evolution of the current architecture of the mitoribosome. Although most of the mito-specific MRPs and extensions of homologous MRPs are situated on the peripheral regions, they also contribute significantly to the formation of linings of the mRNA and tRNA paths, suggesting a tailor-made structural organization of the mito-SSU for the recruitment of mito-specific mRNAs, most of which do not possess a 5' leader sequence. In addition, docking of previously published coordinates of the large (39S) subunit (LSU) into the cryo-EM map of the 55S mitoribosome reveals that mito-specific MRPs of both the SSU and LSU are involved directly in the formation of six of the 15 intersubunit bridges.
History
DepositionApr 1, 2014-
Header (metadata) releaseJun 18, 2014-
Map releaseJun 18, 2014-
UpdateJan 20, 2016-
Current statusJan 20, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0002
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0002
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jd5
  • Surface level: 0.0002
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5941.gif

Downloads & links

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Map

FileDownload / File: emd_5941.map.gz / Format: CCP4 / Size: 196.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmammalian mito-ribosome small subunit structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 375 pix.
= 438.75 Å		1.17 Å/pix.
x 375 pix.
= 438.75 Å		1.17 Å/pix.
x 375 pix.
= 438.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00017 / Movie #1: 0.0002
Minimum - Maximum-0.00045582 - 0.00073399
Average (Standard dev.)0.00000498 (±0.00003911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-188-188-188
Dimensions375375375
Spacing375375375
CellA=B=C: 438.74997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.171.171.17
M x/y/z375375375
origin x/y/z0.0000.0000.000
length x/y/z438.750438.750438.750
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-188-188-188
NC/NR/NS375375375
D min/max/mean-0.0000.0010.000

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Supplemental data

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Sample components

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Entire : small subunit of mito-ribosome

EntireName: small subunit of mito-ribosome
Components
  • Sample: small subunit of mito-ribosome
  • Complex: mito-ribosomal small subunit

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Supramolecule #1000: small subunit of mito-ribosome

SupramoleculeName: small subunit of mito-ribosome / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: 1 / Number unique components: 1
Molecular weightTheoretical: 1.18 MDa

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Supramolecule #1: mito-ribosomal small subunit

SupramoleculeName: mito-ribosomal small subunit / type: complex / ID: 1 / Name.synonym: 28S mito-ribosome / Details: Single particle Cryo-EM of mito-ribosome / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: SSU 40S
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: liver / Organelle: mitochondrion
Molecular weightTheoretical: 1.18 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.86 mg/mL
BufferpH: 7.6
Details: 20 mM HEPES-KOH, pH 7.6, 20 mM MgCl2, 40 mM KCl, 20 mM DTT
GridDetails: 300 mesh Quantifoil holey carbon copper grid, carbon support, glow discharged in a plasma cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeJEOL 3200FS
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateOct 10, 2009
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 0.5 µm / Number real images: 866553 / Average electron dose: 9 e/Å2 / Camera length: 800 / Od range: 1.4 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59717 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsA total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classification, ~28% of the particles - those with low cross-correlation coefficient values with the 55S reference projections - were removed. 307556 particle images were included in the final reconstruction.
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 307556
Final angle assignmentDetails: SPIDER: theta 45 degrees, phi 45 degrees
Final two d classificationNumber classes: 6

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