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- EMDB-50129: Mammalian quaternary complex of a translating 80S ribosome, NAC, ... -

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Entry
Database: EMDB / ID: EMD-50129
TitleMammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK - local refinement
Map datamap of the quaternary RNC-NAC-MetAP1-NatAE-HYPK complex refined with a mask on NatA/E-NAC-MetAP1
Sample
  • Complex: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK
    • Complex: Rabbit ribosome-nascent chain complex
    • Complex: Human NAC heterodimer
    • Complex: Human NatA/E-HYPK complex
      • Complex: Human NatA complex
      • Complex: Human HYPK
      • Complex: Human NatE with GST tag
Keywordstranslation / ribosome / NAC / N-terminal acetyltransferase / NatA / NatE / MetAP1 / HYPK
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.75 Å
AuthorsYudin D / Scaiola A / Ban N
Funding support United States, Germany, Switzerland, European Union, 5 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR35 GM136321 United States
German Research Foundation (DFG)SFB969/A01 and A07 Germany
Swiss National Science Foundation310030_212308 Switzerland
Swiss National Science Foundation51NF40-205601 Switzerland
European Research Council (ERC)Synergy Grant 101072047European Union
CitationJournal: Nature / Year: 2024
Title: NAC guides a ribosomal multienzyme complex for nascent protein processing.
Authors: Alfred M Lentzsch / Denis Yudin / Martin Gamerdinger / Sowmya Chandrasekar / Laurenz Rabl / Alain Scaiola / Elke Deuerling / Nenad Ban / Shu-Ou Shan /
Abstract: Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), ...Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively. Both modifications are strictly cotranslational and essential in higher eukaryotic organisms. The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.
History
DepositionApr 18, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50129.png

Downloads & links

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Map

FileDownload / File: emd_50129.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of the quaternary RNC-NAC-MetAP1-NatAE-HYPK complex refined with a mask on NatA/E-NAC-MetAP1
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 560 pix.
= 593.6 Å		1.06 Å/pix.
x 560 pix.
= 593.6 Å		1.06 Å/pix.
x 560 pix.
= 593.6 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.20138386 - 0.5516588
Average (Standard dev.)0.0016283634 (±0.018514024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 593.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50129_msk_1.map
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Mask #2

Fileemd_50129_msk_2.map
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Additional map: main map lowpass filtered to 8 A resolution

Fileemd_50129_additional_1.map
Annotationmain map lowpass filtered to 8 A resolution
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Additional map: resampled map used during the refinement of the...

Fileemd_50129_additional_2.map
Annotationresampled map used during the refinement of the quaternary complex model - see the methods section of the manuscript for details
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Half map: halfmap A

Fileemd_50129_half_map_1.map
Annotationhalfmap A
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Half map: halfmap B

Fileemd_50129_half_map_2.map
Annotationhalfmap B
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Sample components

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Entire : Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and...

EntireName: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK
Components
  • Complex: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK
    • Complex: Rabbit ribosome-nascent chain complex
    • Complex: Human NAC heterodimer
    • Complex: Human NatA/E-HYPK complex
      • Complex: Human NatA complex
      • Complex: Human HYPK
      • Complex: Human NatE with GST tag

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Supramolecule #1: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and...

SupramoleculeName: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#91
Molecular weightTheoretical: 3.50 MDa

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Supramolecule #2: Rabbit ribosome-nascent chain complex

SupramoleculeName: Rabbit ribosome-nascent chain complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6, #14-#91
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Human NAC heterodimer

SupramoleculeName: Human NAC heterodimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Human NatA/E-HYPK complex

SupramoleculeName: Human NatA/E-HYPK complex / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #10-#13

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Supramolecule #5: Human NatA complex

SupramoleculeName: Human NatA complex / type: complex / ID: 5 / Parent: 4 / Macromolecule list: #11-#12
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Human HYPK

SupramoleculeName: Human HYPK / type: complex / ID: 6 / Parent: 4 / Macromolecule list: #13
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Human NatE with GST tag

SupramoleculeName: Human NatE with GST tag / type: complex / ID: 7 / Parent: 4 / Macromolecule list: #10
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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