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- EMDB-3784: Structure of the membrane-bound human mitoribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3784
TitleStructure of the membrane-bound human mitoribosome
Map dataStructure of the membrane-bound human mitoribosome in isolated mitochondria
Sample
  • Organelle or cellular component: Whole mitochondria purified from human cell culture
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsEnglmeier R / Pfeffer S / Foerster F
Funding support Germany, Netherlands, 3 items
OrganizationGrant numberCountry
German Research FoundationFO 716/4-1 Germany
Nederland Wetenschappelijke organizationVici 724.016.001 Netherlands
German Research FoundationGRK1721 Germany
CitationJournal: Structure / Year: 2017
Title: Structure of the Human Mitochondrial Ribosome Studied In Situ by Cryoelectron Tomography.
Authors: Robert Englmeier / Stefan Pfeffer / Friedrich Förster /
Abstract: Mitochondria maintain their own genome and its corresponding protein synthesis machine, the mitochondrial ribosome (mitoribosome). Mitoribosomes primarily synthesize highly hydrophobic proteins ...Mitochondria maintain their own genome and its corresponding protein synthesis machine, the mitochondrial ribosome (mitoribosome). Mitoribosomes primarily synthesize highly hydrophobic proteins of the inner mitochondrial membrane. Recent studies revealed the complete structure of the isolated mammalian mitoribosome, but its mode of membrane association remained hypothetical. In this study, we used cryoelectron tomography to visualize human mitoribosomes in isolated mitochondria. The subtomogram average of the membrane-associated human mitoribosome reveals a single major contact site with the inner membrane, mediated by the mitochondria-specific protein mL45. A second rRNA-mediated contact site that is present in yeast is absent in humans, resulting in a more variable association of the human mitoribosome with the inner membrane. Despite extensive structural differences of mammalian and fungal mitoribosomal structure, the principal organization of peptide exit tunnel and the mL45 homolog remains invariant, presumably to align the mitoribosome with the membrane-embedded insertion machinery.
History
DepositionJul 6, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseOct 18, 2017-
UpdateNov 18, 2020-
Current statusNov 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0231
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0231
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_3784.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the membrane-bound human mitoribosome in isolated mitochondria
Voxel sizeX=Y=Z: 5.24 Å
Density
Contour LevelBy AUTHOR: 0.0231 / Movie #1: 0.0231
Minimum - Maximum-0.06172496 - 0.11727364
Average (Standard dev.)0.0015579415 (±0.01258275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 576.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.245.245.24
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z576.400576.400576.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean-0.0620.1170.002

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Supplemental data

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Sample components

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Entire : Whole mitochondria purified from human cell culture

EntireName: Whole mitochondria purified from human cell culture
Components
  • Organelle or cellular component: Whole mitochondria purified from human cell culture

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Supramolecule #1: Whole mitochondria purified from human cell culture

SupramoleculeName: Whole mitochondria purified from human cell culture / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HEK-293 / Organelle: Mitochondria

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.2 sec. / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 51 / Number images used: 7796 / Reference model: reference-free template / Software - Name: PyTom
CTF correctionSoftware - Name: PyTom
Final 3D classificationSoftware - Name: PyTom
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PyTom / Number subtomograms used: 663

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Atomic model buiding 1

RefinementProtocol: OTHER

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