9RSX | pdb_00009rsx

Structure of RACK1 bound to the C-terminus of SERBP1 and the RIH region of ZAK

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-07-01 Released: 2025-12-10 
  • Deposition Author(s): Niu, S., Beckmann, R.
  • Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

ZAK activation at the collided ribosome.

Huso, V.L.Niu, S.Catipovic, M.A.Saba, J.A.Denk, T.Park, E.Cheng, J.Berninghausen, O.Becker, T.Green, R.Beckmann, R.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09772-8
  • Primary Citation of Related Structures:  
    9RPV, 9RSX

  • PubMed 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 1 . 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.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 20A [auth N2]800Homo sapiensMutation(s): 0 
EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYL2 (Homo sapiens)
Explore Q9NYL2 
Go to UniProtKB:  Q9NYL2
PHAROS:  Q9NYL2
GTEx:  ENSG00000091436 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYL2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plasminogen activator inhibitor 1 RNA-binding proteinB [auth N3]408Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NC51 (Homo sapiens)
Explore Q8NC51 
Go to UniProtKB:  Q8NC51
PHAROS:  Q8NC51
GTEx:  ENSG00000142864 
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UniProt GroupQ8NC51
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3C [auth RD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
UniProt & NIH Common Fund Data Resources
Find proteins for P23396 (Homo sapiens)
Explore P23396 
Go to UniProtKB:  P23396
PHAROS:  P23396
GTEx:  ENSG00000149273 
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UniProt GroupP23396
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1D [auth Rg]317Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63244 (Homo sapiens)
Explore P63244 
Go to UniProtKB:  P63244
PHAROS:  P63244
GTEx:  ENSG00000204628 
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UniProt GroupP63244
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release