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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 / stalled ribosome sensor activity / negative regulation of translation in response to endoplasmic reticulum stress / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / ribosome hibernation / translation elongation factor binding / PML body organization ...positive regulation of mitotic DNA damage checkpoint / negative regulation of stress-activated protein kinase signaling cascade / stalled ribosome sensor activity / negative regulation of translation in response to endoplasmic reticulum stress / GCN2-mediated signaling / cell death / mitogen-activated protein kinase kinase kinase / ribosome hibernation / translation elongation factor binding / PML body organization / JUN kinase kinase kinase activity / SUMO binding / protein kinase regulator activity / stress-activated protein kinase signaling cascade / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / positive regulation of programmed cell death / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / limb development / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / regulation of mitotic metaphase/anaphase transition / supercoiled DNA binding / embryonic digit morphogenesis / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to UV-B / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / protein kinase A binding / ion channel inhibitor activity / p38MAPK cascade / Ribosomal scanning and start codon recognition / pyroptotic inflammatory response / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / negative regulation of translational frameshifting / BH3 domain binding / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell division / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of GTPase activity / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / MAP kinase kinase kinase activity / protein kinase activator activity / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / stress-activated MAPK cascade / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of protein binding / positive regulation of intrinsic apoptotic signaling pathway / spindle assembly / JNK cascade / translation repressor activity / translation regulator activity / gastrulation / cytoskeleton organization / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / positive regulation of microtubule polymerization / signaling adaptor activity / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / rescue of stalled cytosolic ribosome / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / SH2 domain binding / tubulin binding / protein kinase C binding / cyclin binding / DNA damage checkpoint signaling
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 / Small (40S) ribosomal subunit Asc1/RACK1 / Sterile alpha motif/pointed domain superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / 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: 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
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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