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- EMDB-2876: The structure of the human mitochondrial ribosome (class 1). -

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Basic information

Entry
Database: EMDB / ID: EMD-2876
TitleThe structure of the human mitochondrial ribosome (class 1).
Map dataHuman mitochondrial ribosome, class 1
Sample
  • Sample: Human mitochondrial ribosome, class 1.
  • Complex: Mitochondrial ribosome
KeywordsMitochondrial ribosome / 55S / translation
Function / homology
Function and homology information


mitochondrial ribosome binding / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation ...mitochondrial ribosome binding / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA processing / large ribosomal subunit rRNA binding / double-stranded RNA binding / regulation of translation / ribosomal large subunit assembly / large ribosomal subunit / cell junction / small ribosomal subunit / endonuclease activity / nuclear membrane / cell population proliferation / mitochondrial inner membrane / tRNA binding / negative regulation of translation / nuclear body / ribosome / rRNA binding / structural constituent of ribosome / mitochondrial matrix / cell cycle / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / synapse / apoptotic process / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / PPR repeat family / 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 ...Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / PPR repeat family / 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 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / 40S ribosomal protein rpS2 (S5p), N-terminal / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein L37, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S24/S35, mitochondrial, conserved domain / Ribosomal protein S30, mitochondrial / Mitochondrial ribosomal subunit protein / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Tim44-like domain / Tim44 / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Ribosomal protein L49/IMG2 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial large subunit ribosomal protein (Img2) / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Ribonuclease III / TGS domain profile. / TGS / TGS-like / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Large ribosomal subunit protein mL52 / Mitochondrial ribosomal protein L18, isoform CRA_b / Large ribosomal subunit protein uL22m / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 ...Large ribosomal subunit protein mL52 / Mitochondrial ribosomal protein L18, isoform CRA_b / Large ribosomal subunit protein uL22m / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS9m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / : / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL55 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein uL30m / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein uL24m / Small ribosomal subunit protein mS37 / Large ribosomal subunit protein mL38 / Small ribosomal subunit protein uS3m / Large ribosomal subunit protein mL53 / Small ribosomal subunit protein mS39 / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Small ribosomal subunit protein mS26 / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL66 / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS2m / Large ribosomal subunit protein uL11m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS40 / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAmunts A / Brown A / Toots J / Scheres SH / Ramakrishnan V
CitationJournal: Science / Year: 2015
Title: Ribosome. The structure of the human mitochondrial ribosome.
Authors: Alexey Amunts / Alan Brown / Jaan Toots / Sjors H W Scheres / V Ramakrishnan /
Abstract: The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact ...The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.
History
DepositionFeb 8, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseMar 18, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9m
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2876.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman mitochondrial ribosome, class 1
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.5883528 - 0.97279251
Average (Standard dev.)0.00214477 (±0.02912913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z428.800428.800428.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.5880.9730.002

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Supplemental data

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Supplemental map: Class1 half1.map

FileClass1_half1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: Class1 half2.map

FileClass1_half2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Human mitochondrial ribosome, class 1.

EntireName: Human mitochondrial ribosome, class 1.
Components
  • Sample: Human mitochondrial ribosome, class 1.
  • Complex: Mitochondrial ribosome

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Supramolecule #1000: Human mitochondrial ribosome, class 1.

SupramoleculeName: Human mitochondrial ribosome, class 1. / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Multimer / Number unique components: 1
Molecular weightExperimental: 2.7 MDa / Theoretical: 2.7 MDa / Method: Sedimentation

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Supramolecule #1: Mitochondrial ribosome

SupramoleculeName: Mitochondrial ribosome / type: complex / ID: 1 / Name.synonym: 55S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Homo sapiens (human) / synonym: human / Tissue: kidney / Cell: HEK 293 / Organelle: mitochondria / Location in cell: Inner mitochondrial membrane
Molecular weightExperimental: 2.7 MDa / Theoretical: 2.7 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

Concentration0.23 mg/mL
BufferpH: 7.45
Details: 20 mM Hepes-KOH pH 7.45, 100 mM KCl, 20 mM MgOAc, 2 mM DTT
GridDetails: 30 s on glow-discharged holey carbon grids (Quantifoil R2/2), onto which a home-made continuous carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK II / Method: Blot 2.5 seconds before plunging

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Electron microscopy #1

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Microscopy ID1
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateApr 3, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 7526 / Average electron dose: 25 e/Å2
Details: Every image is the average of 17 frames recorded by the direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #2

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Microscopy ID2
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateApr 11, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 7526 / Average electron dose: 25 e/Å2
Details: Every image is the average of 17 frames recorded by the direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #3

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Microscopy ID3
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateMay 10, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 7526 / Average electron dose: 25 e/Å2
Details: Every image is the average of 17 frames recorded by the direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #4

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Microscopy ID4
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateMay 30, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 7526 / Average electron dose: 25 e/Å2
Details: Every image is the average of 17 frames recorded by the direct electron detector
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION / Number images used: 884122
DetailsData were processed in Relion to compensate for beam-induced movement.
FSC plot (resolution estimation)

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