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- EMDB-17721: human mitoribosomal large subunit assembly intermediate 3 with GTPBP5 -

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Basic information

Entry
Database: EMDB / ID: EMD-17721
Titlehuman mitoribosomal large subunit assembly intermediate 3 with GTPBP5
Map datafull map, sharpened
Sample
  • Complex: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module
Keywordsmitochondria / maturation / biogenesis / ribosome / GTPBP5 / OBGH1 / LSU
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsKummer E / Nguyen TG
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0067360 Denmark
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome.
Authors: Thu Giang Nguyen / Christina Ritter / Eva Kummer /
Abstract: Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ...Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria.
History
DepositionJun 23, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17721.png

Downloads & links

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Map

FileDownload / File: emd_17721.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map, sharpened
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 480 pix.
= 518.4 Å		1.08 Å/pix.
x 480 pix.
= 518.4 Å		1.08 Å/pix.
x 480 pix.
= 518.4 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.765
Minimum - Maximum-2.3692756 - 5.429064
Average (Standard dev.)-0.0034437985 (±0.1908161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17721_msk_1.map
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Additional map: full map, unsharpened

Fileemd_17721_additional_1.map
Annotationfull map, unsharpened
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Half map: #1

Fileemd_17721_half_map_1.map
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Half map: #2

Fileemd_17721_half_map_2.map
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Sample components

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Entire : large mitoribosomal subunit biogenesis intermediate with GTPBP10,...

EntireName: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module
Components
  • Complex: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module

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Supramolecule #1: large mitoribosomal subunit biogenesis intermediate with GTPBP10,...

SupramoleculeName: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#58
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.9 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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7odt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39296
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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