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- EMDB-44460: 80S ribosome with H13A angiogenin and tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-44460
Title80S ribosome with H13A angiogenin and tRNA
Map data80S ribosome with H13A angiogenin and tRNA
Sample
  • Complex: 80S ribosome with H13A angiogenin and tRNA
    • Complex: 80S ribosome
    • Complex: H13A angiogenin
    • Complex: tRNA-fMet
    • Complex: tRNA from in vitro transcription system
    • Complex: mRNA
KeywordsAngiogenin / RNase / RIBOSOME
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human) / Escherichia coli (E. coli) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLoveland AB / Korostelev AA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM127094 United States
CitationJournal: Nature / Year: 2024
Title: Structural mechanism of angiogenin activation by the ribosome.
Authors: Anna B Loveland / Cha San Koh / Robin Ganesan / Allan Jacobson / Andrei A Korostelev /
Abstract: Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, ...Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases.
History
DepositionApr 12, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44460.png

Downloads & links

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Map

FileDownload / File: emd_44460.map.gz / Format: CCP4 / Size: 857.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation80S ribosome with H13A angiogenin and tRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 608 pix.
= 504.64 Å		0.83 Å/pix.
x 608 pix.
= 504.64 Å		0.83 Å/pix.
x 608 pix.
= 504.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-8.101321 - 18.936764
Average (Standard dev.)0.009524148 (±1.138087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions608608608
Spacing608608608
CellA=B=C: 504.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 80S ribosome with H13A angiogenin and tRNA, low-pass...

Fileemd_44460_additional_1.map
Annotation80S ribosome with H13A angiogenin and tRNA, low-pass filtered to 5 A, used to visualize tRNA
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 80S ribosome with H13A angiogenin and tRNA, half map 1

Fileemd_44460_half_map_1.map
Annotation80S ribosome with H13A angiogenin and tRNA, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 80S ribosome with H13A angiogenin and tRNA, half map 2

Fileemd_44460_half_map_2.map
Annotation80S ribosome with H13A angiogenin and tRNA, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S ribosome with H13A angiogenin and tRNA

EntireName: 80S ribosome with H13A angiogenin and tRNA
Components
  • Complex: 80S ribosome with H13A angiogenin and tRNA
    • Complex: 80S ribosome
    • Complex: H13A angiogenin
    • Complex: tRNA-fMet
    • Complex: tRNA from in vitro transcription system
    • Complex: mRNA

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Supramolecule #1: 80S ribosome with H13A angiogenin and tRNA

SupramoleculeName: 80S ribosome with H13A angiogenin and tRNA / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 4.5 MDa

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Supramolecule #2: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Reticulocyte

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Supramolecule #3: H13A angiogenin

SupramoleculeName: H13A angiogenin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: tRNA-fMet

SupramoleculeName: tRNA-fMet / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #5: tRNA from in vitro transcription system

SupramoleculeName: tRNA from in vitro transcription system / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #6: mRNA

SupramoleculeName: mRNA / type: complex / ID: 6 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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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
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 451181
Startup modelType of model: EMDB MAP
EMDB ID:

4729

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2613
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN
Final 3D classificationNumber classes: 4 / Avg.num./class: 3000 / Software - Name: FREALIGN
FSC plot (resolution estimation)

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