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- EMDB-54148: Local refined cryo-EM map focusing on ZAK-RACK1 of the stalled 80S -

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Basic information

Entry
Database: EMDB / ID: EMD-54148
TitleLocal refined cryo-EM map focusing on ZAK-RACK1 of the stalled 80S
Map dataLocal filtered map focusing on ZAK-RACK1 of the stalled 80S
Sample
  • Complex: ZAK-bound H. sapiens disome - focusing on ZAK-RACK1 of the stalled 80S
KeywordsZAK / collision / RSR / quality control / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsNiu S / Beckmann R
Funding support1 items
OrganizationGrant numberCountry
European Research Council (ERC)
CitationJournal: Nature / Year: 2025
Title: ZAK activation at the collided ribosome.
Authors: Vienna L Huso / Shuangshuang Niu / Marco A Catipovic / James A Saba / Timo Denk / Eugene Park / Jingdong Cheng / Otto Berninghausen / Thomas Becker / Rachel Green / Roland Beckmann /
Abstract: Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK. ...Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.
History
DepositionJun 24, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54148.png

Downloads & links

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Map

FileDownload / File: emd_54148.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered map focusing on ZAK-RACK1 of the stalled 80S
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 500 pix.
= 581.6 Å		1.16 Å/pix.
x 500 pix.
= 581.6 Å		1.16 Å/pix.
x 500 pix.
= 581.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-4.3338456 - 7.925731
Average (Standard dev.)0.0004151206 (±0.035923976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 581.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local refined map focusing on ZAK-RACK1 of the stalled 80S

Fileemd_54148_additional_1.map
AnnotationLocal refined map focusing on ZAK-RACK1 of the stalled 80S
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap A from focused refinement on ZAK-RACK1 of the stalled 80S

Fileemd_54148_half_map_1.map
AnnotationHalfmap A from focused refinement on ZAK-RACK1 of the stalled 80S
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap B from focused refinement on ZAK-RACK1 of the stalled 80S

Fileemd_54148_half_map_2.map
AnnotationHalfmap B from focused refinement on ZAK-RACK1 of the stalled 80S
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ZAK-bound H. sapiens disome - focusing on ZAK-RACK1 of the stalled 80S

EntireName: ZAK-bound H. sapiens disome - focusing on ZAK-RACK1 of the stalled 80S
Components
  • Complex: ZAK-bound H. sapiens disome - focusing on ZAK-RACK1 of the stalled 80S

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Supramolecule #1: ZAK-bound H. sapiens disome - focusing on ZAK-RACK1 of the stalled 80S

SupramoleculeName: ZAK-bound H. sapiens disome - focusing on ZAK-RACK1 of the stalled 80S
type: complex / ID: 1 / Parent: 0
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123142
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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