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- EMDB-54236: Structure of RACK1 bound to the C-terminus of SERBP1 and the RIH ... -

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Entry
Database: EMDB / ID: EMD-54236
TitleStructure of RACK1 bound to the C-terminus of SERBP1 and the RIH region of ZAK
Map dataLocal filtered cryo-EM map focusing on RACK1 of the hybrid state translating 80S
Sample
  • Complex: RACK1 bound to ZAK(RIH) and SERBP1(C-term)
    • Protein or peptide: Mitogen-activated protein kinase kinase kinase 20
    • Protein or peptide: Plasminogen activator inhibitor 1 RNA-binding protein
    • Protein or peptide: 40S ribosomal protein S3
    • Protein or peptide: Receptor of activated protein C kinase 1
KeywordsZAK / collision / RSR / quality control / RIBOSOME
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 / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / limb development / TNFR1-mediated ceramide production / negative regulation of DNA repair / regulation of mitotic metaphase/anaphase transition / supercoiled DNA binding / NF-kappaB complex / embryonic digit morphogenesis / 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 / Ribosomal scanning and start codon recognition / p38MAPK cascade / 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 / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / protein serine/threonine kinase inhibitor activity / 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 / tubulin binding / SH2 domain binding / cyclin binding / protein kinase C 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsNiu S / Beckmann R
Funding supportEuropean Union, 1 items
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, 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_54236.png

Downloads & links

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Map

FileDownload / File: emd_54236.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered cryo-EM map focusing on RACK1 of the hybrid state translating 80S
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 640 pix.
= 465.28 Å		0.73 Å/pix.
x 640 pix.
= 465.28 Å		0.73 Å/pix.
x 640 pix.
= 465.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-3.7195585 - 6.983495
Average (Standard dev.)0.00014663479 (±0.028428262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 465.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map from local refinement on the RACK1 region

Fileemd_54236_additional_1.map
AnnotationMap from local refinement on the RACK1 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap B for the local refinement on the RACK1 region

Fileemd_54236_half_map_1.map
AnnotationHalfmap B for the local refinement on the RACK1 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap A for the local refinement on the RACK1 region

Fileemd_54236_half_map_2.map
AnnotationHalfmap A for the local refinement on the RACK1 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RACK1 bound to ZAK(RIH) and SERBP1(C-term)

EntireName: RACK1 bound to ZAK(RIH) and SERBP1(C-term)
Components
  • Complex: RACK1 bound to ZAK(RIH) and SERBP1(C-term)
    • Protein or peptide: Mitogen-activated protein kinase kinase kinase 20
    • Protein or peptide: Plasminogen activator inhibitor 1 RNA-binding protein
    • Protein or peptide: 40S ribosomal protein S3
    • Protein or peptide: Receptor of activated protein C kinase 1

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Supramolecule #1: RACK1 bound to ZAK(RIH) and SERBP1(C-term)

SupramoleculeName: RACK1 bound to ZAK(RIH) and SERBP1(C-term) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitogen-activated protein kinase kinase kinase 20

MacromoleculeName: Mitogen-activated protein kinase kinase kinase 20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: mitogen-activated protein kinase kinase kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.284078 KDa
SequenceString: MSSLGASFVQ IKFDDLQFFE NCGGGSFGSV YRAKWISQDK EVAVKKLLKI EKEAEILSVL SHRNIIQFYG VILEPPNYGI VTEYASLGS LYDYINSNRS EEMDMDHIMT WATDVAKGMH YLHMEAPVKV IHRDLKSRNV VIAADGVLKI CDFGASRFHN H TTHMSLVG ...String:
MSSLGASFVQ IKFDDLQFFE NCGGGSFGSV YRAKWISQDK EVAVKKLLKI EKEAEILSVL SHRNIIQFYG VILEPPNYGI VTEYASLGS LYDYINSNRS EEMDMDHIMT WATDVAKGMH YLHMEAPVKV IHRDLKSRNV VIAADGVLKI CDFGASRFHN H TTHMSLVG TFPWMAPEVI QSLPVSETCD TYSYGVVLWE MLTREVPFKG LEGLQVAWLV VEKNERLTIP SSCPRSFAEL LH QCWEADA KKRPSFKQII SILESMSNDT SLPDKCNSFL HNKAEWRCEI EATLERLKKL ERDLSFKEQE LKERERRLKM WEQ KLTEQS NTPLLPSFEI GAWTEDDVYC WVQQLVRKGD SSAEMSVYAS LFKENNITGK RLLLLEEEDL KDMGIVSKGH IIHF KSAIE KLTHDYINLF HFPPLIKDSG GEPEENEEKI VNLELVFGFH LKPGTGPQDC KWKMYMEMDG DEIAITYIKD VTFNT NLPD AEILKMTKPP FVMEKWIVGI AKSQTVECTV TYESDVRTPK STKHVHSIQW SRTKPQDEVK AVQLAIQTLF TNSDGN PGS RSDSSADCQW LDTLRMRQIA SNTSLQRSQS NPILGSPFFS HFDGQDSYAA AVRRPQVPIK YQQITPVNQS RSSSPTQ YG LTKNFSSLHL NSRDSGFSSG NTDTSSERGR YSDRSRNKYG RGSISLNSSP RGRYSGKSQH STPSRGRYPG KFYRVSQS A LNPHQSPDFK RSPRDLHQPN TIPGMPLHPE TDSRASEEDS KVSEGGWTKV EYRKKPHRPS PAKTNKERAR GDHRGWRNF

UniProtKB: Mitogen-activated protein kinase kinase kinase 20

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Macromolecule #2: Plasminogen activator inhibitor 1 RNA-binding protein

MacromoleculeName: Plasminogen activator inhibitor 1 RNA-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.051504 KDa
SequenceString: MPGHLQEGFG CVVTNRFDQL FDDESDPFEV LKAAENKKKE AGGGGVGGPG AKSAAQAAAQ TNSNAAGKQL RKESQKDRKN PLPPSVGVV DKKEETQPPV ALKKEGIRRV GRRPDQQLQG EGKIIDRRPE RRPPRERRFE KPLEEKGEGG EFSVDRPIID R PIRGRGGL ...String:
MPGHLQEGFG CVVTNRFDQL FDDESDPFEV LKAAENKKKE AGGGGVGGPG AKSAAQAAAQ TNSNAAGKQL RKESQKDRKN PLPPSVGVV DKKEETQPPV ALKKEGIRRV GRRPDQQLQG EGKIIDRRPE RRPPRERRFE KPLEEKGEGG EFSVDRPIID R PIRGRGGL GRGRGGRGRG MGRGDGFDSR GKREFDRHSG SDRSSFSHYS GLKHEDKRGG SGSHNWGTVK DELTESPKYI QK QISYNYS DLDQSNVTEE TPEGEEHHPV ADTENKENEV EEVKEEGPKE MTLDEWKAIQ NKDRAKVEFN IRKPNEGADG QWK KGFVLH KSKSEEAHAE DSVMDHHFRK PANDITSQLE INFGDLGRPG RGGRGGRGGR GRGGRPNRGS RTDKSSASAP DVDD PEAFP ALA

UniProtKB: SERPINE1 mRNA-binding protein 1

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Macromolecule #3: 40S ribosomal protein S3

MacromoleculeName: 40S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-(apurinic or apyrimidinic site) lyase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.729369 KDa
SequenceString: MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV ...String:
MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV DTAVRHVLLR QGVLGIKVKI MLPWDPTGKI GPKKPLPDHV SIVEPKDEIL PTTPISEQKG GKPEPPAMPQ PV PTA

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #4: Receptor of activated protein C kinase 1

MacromoleculeName: Receptor of activated protein C kinase 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.115652 KDa
SequenceString: MTEQMTLRGT LKGHNGWVTQ IATTPQFPDM ILSASRDKTI IMWKLTRDET NYGIPQRALR GHSHFVSDVV ISSDGQFALS GSWDGTLRL WDLTTGTTTR RFVGHTKDVL SVAFSSDNRQ IVSGSRDKTI KLWNTLGVCK YTVQDESHSE WVSCVRFSPN S SNPIIVSC ...String:
MTEQMTLRGT LKGHNGWVTQ IATTPQFPDM ILSASRDKTI IMWKLTRDET NYGIPQRALR GHSHFVSDVV ISSDGQFALS GSWDGTLRL WDLTTGTTTR RFVGHTKDVL SVAFSSDNRQ IVSGSRDKTI KLWNTLGVCK YTVQDESHSE WVSCVRFSPN S SNPIIVSC GWDKLVKVWN LANCKLKTNH IGHTGYLNTV TVSPDGSLCA SGGKDGQAML WDLNEGKHLY TLDGGDIINA LC FSPNRYW LCAATGPSIK IWDLEGKIIV DELKQEVIST SSKAEPPQCT SLAWSADGQT LFAGYTDNLV RVWQVTIGTR

UniProtKB: Small ribosomal subunit protein RACK1

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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: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 108673
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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