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- EMDB-22209: Structure of bovine 55S mitochondrial ribosome -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-22209
TitleStructure of bovine 55S mitochondrial ribosome
Map dataBovine 55S mt ribosome
Sample
  • Complex: Bovine mitochondrial 55S ribosome
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsSharma MR / Koripella RK / Agrawal RK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 GM61576 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation.
Authors: Ravi Kiran Koripella / Manjuli R Sharma / Kalpana Bhargava / Partha P Datta / Prem S Kaushal / Pooja Keshavan / Linda L Spremulli / Nilesh K Banavali / Rajendra K Agrawal /
Abstract: The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we ...The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1 in mitochondrial tRNA (tRNA) translocation. In particular, the mito-specific C-terminal extension in EF-G1 is directly involved in translocation of the acceptor arm of the A-site tRNA. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane.
History
DepositionJun 23, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateAug 12, 2020-
Current statusAug 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22209.png

Downloads & links

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Map

FileDownload / File: emd_22209.map.gz / Format: CCP4 / Size: 105.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBovine 55S mt ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 302 pix.
= 501.32 Å		1.66 Å/pix.
x 302 pix.
= 501.32 Å		1.66 Å/pix.
x 302 pix.
= 501.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.073014244 - 0.13210529
Average (Standard dev.)0.0007530704 (±0.006033121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions302302302
Spacing302302302
CellA=B=C: 501.31998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z302302302
origin x/y/z0.0000.0000.000
length x/y/z501.320501.320501.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS302302302
D min/max/mean-0.0730.1320.001

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Supplemental data

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Sample components

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Entire : Bovine mitochondrial 55S ribosome

EntireName: Bovine mitochondrial 55S ribosome
Components
  • Complex: Bovine mitochondrial 55S ribosome

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Supramolecule #1: Bovine mitochondrial 55S ribosome

SupramoleculeName: Bovine mitochondrial 55S ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (cattle) / Organ: Liver

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.6
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 69.21 e/Å2 / #1 - Image recording ID: 2
#1 - Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)
#1 - Detector mode: COUNTING / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j9m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25038
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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