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- PDB-9rsx: Structure of RACK1 bound to the C-terminus of SERBP1 and the RIH ... -

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Basic information

Entry
Database: PDB / ID: 9rsx
TitleStructure of RACK1 bound to the C-terminus of SERBP1 and the RIH region of ZAK
Components
  • 40S ribosomal protein S3
  • Mitogen-activated protein kinase kinase kinase 20
  • Plasminogen activator inhibitor 1 RNA-binding protein
  • Receptor of activated protein C kinase 1
KeywordsRIBOSOME / ZAK / collision / RSR / quality control
Function / homology
Function and homology information


positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / negative regulation of translation in response to endoplasmic reticulum stress / stalled ribosome sensor activity / GCN2-mediated signaling / cell death / PML body organization / mitogen-activated protein kinase kinase kinase / translation elongation factor binding / ribosome hibernation ...positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / negative regulation of translation in response to endoplasmic reticulum stress / stalled ribosome sensor activity / GCN2-mediated signaling / cell death / PML body organization / mitogen-activated protein kinase kinase kinase / translation elongation factor binding / ribosome hibernation / SUMO binding / JUN kinase kinase kinase activity / embryonic digit morphogenesis / negative regulation of endoplasmic reticulum unfolded protein response / stress-activated protein kinase signaling cascade / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of programmed cell death / cellular response to UV-B / IRE1-RACK1-PP2A complex / TNFR1-mediated ceramide production / positive regulation of Golgi to plasma membrane protein transport / regulation of mitotic metaphase/anaphase transition / positive regulation of DNA-templated transcription initiation / negative regulation of DNA repair / supercoiled DNA binding / regulation of establishment of cell polarity / oxidized purine DNA binding / NF-kappaB complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / p38MAPK cascade / ubiquitin-like protein conjugating enzyme binding / cytoplasmic translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / protein kinase A binding / Translation initiation complex formation / negative regulation of Wnt signaling pathway / BH3 domain binding / limb development / negative regulation of translational frameshifting / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SARS-CoV-1 modulates host translation machinery / pyroptotic inflammatory response / regulation of cell division / positive regulation of GTPase activity / stress-activated MAPK cascade / MAP kinase kinase kinase activity / Peptide chain elongation / JNK cascade / Selenocysteine synthesis / negative regulation of protein binding / Formation of a pool of free 40S subunits / protein kinase activator activity / protein serine/threonine kinase inhibitor activity / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / DNA damage checkpoint signaling / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / positive regulation of microtubule polymerization / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of mRNA stability / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / negative regulation of protein ubiquitination / translation repressor activity / SH2 domain binding / positive regulation of apoptotic signaling pathway / signaling adaptor activity / Hsp70 protein binding / positive regulation of DNA repair / cyclin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase C binding / chromosome segregation / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / iron-sulfur cluster binding / rescue of stalled cytosolic ribosome / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / negative regulation of smoothened signaling pathway / cellular response to glucose stimulus / TNFR1-induced NF-kappa-B signaling pathway / mRNA 3'-UTR binding / cellular response to reactive oxygen species / DNA endonuclease activity
Similarity search - Function
Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / : / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / WD domain, G-beta repeat / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / G-protein beta WD-40 repeat / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Serine/Threonine protein kinases, catalytic domain / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein uS3 / Small ribosomal subunit protein RACK1 / SERPINE1 mRNA-binding protein 1 / Mitogen-activated protein kinase kinase kinase 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsNiu, S. / Beckmann, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nature / Year: 2026
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
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jan 28, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N2: Mitogen-activated protein kinase kinase kinase 20
N3: Plasminogen activator inhibitor 1 RNA-binding protein
RD: 40S ribosomal protein S3
Rg: Receptor of activated protein C kinase 1


Theoretical massNumber of molelcules
Total (without water)198,1814
Polymers198,1814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 20 / Human cervical cancer suppressor gene 4 protein / HCCS-4 / Leucine zipper- and sterile alpha motif- ...Human cervical cancer suppressor gene 4 protein / HCCS-4 / Leucine zipper- and sterile alpha motif-containing kinase / MLK-like mitogen-activated protein triple kinase / Mitogen-activated protein kinase kinase kinase MLT / Mixed lineage kinase 7 / Mixed lineage kinase-related kinase / MLK-related kinase / MRK / Sterile alpha motif- and leucine zipper-containing kinase AZK


Mass: 91284.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9NYL2, mitogen-activated protein kinase kinase kinase
#2: Protein Plasminogen activator inhibitor 1 RNA-binding protein / PAI1 RNA-binding protein 1 / PAI-RBP1 / SERPINE1 mRNA-binding protein 1


Mass: 45051.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NC51
#3: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#4: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RACK1 bound to ZAK(RIH) and SERBP1(C-term) / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2cryoSPARCparticle selection
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108673 / Symmetry type: POINT

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