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- EMDB-34452: Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex -

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Entry
Database: EMDB / ID: EMD-34452
TitleCryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex
Map data
Sample
  • Complex: KBTBD2-CUL3-Rbx1-p85a dimeric complex
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Kelch repeat and BTB domain-containing protein 2
    • Protein or peptide: Phosphatidylinositol 3-kinase regulatory subunit alpha
    • Protein or peptide: Cullin-3
  • Ligand: ZINC ION
Keywordsligase / complex
Function / homology
Function and homology information


liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / perinuclear endoplasmic reticulum membrane / polar microtubule / regulation of toll-like receptor 4 signaling pathway / anaphase-promoting complex-dependent catabolic process ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / perinuclear endoplasmic reticulum membrane / polar microtubule / regulation of toll-like receptor 4 signaling pathway / anaphase-promoting complex-dependent catabolic process / phosphatidylinositol kinase activity / COPII vesicle coating / phosphatidylinositol 3-kinase regulator activity / cullin-RING-type E3 NEDD8 transferase / stem cell division / positive regulation of focal adhesion disassembly / cellular response to chemical stress / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / NEDD8 transferase activity / RHOBTB3 ATPase cycle / interleukin-18-mediated signaling pathway / cullin-RING ubiquitin ligase complex / PI3K events in ERBB4 signaling / myeloid leukocyte migration / embryonic cleavage / cell projection organization / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of mitotic metaphase/anaphase transition / Cul7-RING ubiquitin ligase complex / phosphatidylinositol 3-kinase regulatory subunit binding / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / cis-Golgi network / RHOF GTPase cycle / kinase activator activity / positive regulation of protein autoubiquitination / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / protein neddylation / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / Notch binding / NEDD8 ligase activity / RND1 GTPase cycle / RHOBTB1 GTPase cycle / Cul5-RING ubiquitin ligase complex / Costimulation by the CD28 family / RND2 GTPase cycle / MET activates PI3K/AKT signaling / ubiquitin-ubiquitin ligase activity / fibroblast apoptotic process / positive regulation of leukocyte migration / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of filopodium assembly / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / growth hormone receptor signaling pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / insulin binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / RHOV GTPase cycle / mitotic metaphase chromosome alignment / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / RHOB GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / stress fiber assembly / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / Prolactin receptor signaling / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / positive regulation of cytokinesis / intracellular glucose homeostasis / protein monoubiquitination / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / cullin family protein binding / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle
Similarity search - Function
Kelch repeat and BTB domain-containing protein 2 / : / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain ...Kelch repeat and BTB domain-containing protein 2 / : / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Kelch / Kelch repeat type 1 / Kelch motif / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Kelch-type beta propeller / Rho GTPase activation protein / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha / E3 ubiquitin-protein ligase RBX1 / Cullin-3 / Kelch repeat and BTB domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsHu Y / Mao Q / Chen Z / Sun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81900729 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3.
Authors: Yuxia Hu / Zhao Zhang / Qiyu Mao / Xiang Zhang / Aihua Hao / Yu Xun / Yeda Wang / Lin Han / Wuqiang Zhan / Qianying Liu / Yue Yin / Chao Peng / Eva Marie Y Moresco / Zhenguo Chen / Bruce Beutler / Lei Sun /
Abstract: Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. ...Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. Cellular levels of the regulatory p85α subunit are tightly controlled by regulated proteasomal degradation. In adipose tissue and growth plates, failure of K48-linked p85α ubiquitination causes diabetes, lipodystrophy and dwarfism in mice, as in humans with SHORT syndrome. Here we elucidated the structures of the key ubiquitin ligase complexes regulating p85α availability. Specificity is provided by the substrate receptor KBTBD2, which recruits p85α to the cullin3-RING E3 ubiquitin ligase (CRL3). CRL3 forms multimers, which disassemble into dimers upon substrate binding (CRL3-p85α) and/or neddylation by the activator NEDD8 (CRL3~N8), leading to p85α ubiquitination and degradation. Deactivation involves dissociation of NEDD8 mediated by the COP9 signalosome and displacement of KBTBD2 by the inhibitor CAND1. The hereby identified structural basis of p85α regulation opens the way to better understanding disturbances of glucose regulation, growth and cancer.
History
DepositionOct 8, 2022-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34452.png

Downloads & links

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Map

FileDownload / File: emd_34452.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.332 Å
Density
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0017728873 - 1.8945361
Average (Standard dev.)0.0005839851 (±0.017095936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 511.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #3

Fileemd_34452_additional_1.map
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Additional map: #2

Fileemd_34452_additional_2.map
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Additional map: #1

Fileemd_34452_additional_3.map
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Half map: #2

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Sample components

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Entire : KBTBD2-CUL3-Rbx1-p85a dimeric complex

EntireName: KBTBD2-CUL3-Rbx1-p85a dimeric complex
Components
  • Complex: KBTBD2-CUL3-Rbx1-p85a dimeric complex
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Kelch repeat and BTB domain-containing protein 2
    • Protein or peptide: Phosphatidylinositol 3-kinase regulatory subunit alpha
    • Protein or peptide: Cullin-3
  • Ligand: ZINC ION

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Supramolecule #1: KBTBD2-CUL3-Rbx1-p85a dimeric complex

SupramoleculeName: KBTBD2-CUL3-Rbx1-p85a dimeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #2: Kelch repeat and BTB domain-containing protein 2

MacromoleculeName: Kelch repeat and BTB domain-containing protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.431375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTQDERQIN TEYAVSLLEQ LKLFYEQQLF TDIVLIVEGT EFPCHKMVLA TCSSYFRAMF MSGLSESKQT HVHLRNVDAA TLQIIITYA YTGNLAMNDS TVEQLYETAC FLQVEDVLQR CREYLIKKIN AENCVRLLSF ADLFSCEELK QSAKRMVEHK F TAVYHQDA ...String:
MSTQDERQIN TEYAVSLLEQ LKLFYEQQLF TDIVLIVEGT EFPCHKMVLA TCSSYFRAMF MSGLSESKQT HVHLRNVDAA TLQIIITYA YTGNLAMNDS TVEQLYETAC FLQVEDVLQR CREYLIKKIN AENCVRLLSF ADLFSCEELK QSAKRMVEHK F TAVYHQDA FMQLSHDLLI DILSSDNLNV EKEETVREAA MLWLEYNTES RSQYLSSVLS QIRIDALSEV TQRAWFQGLP PN DKSVVVQ GLYKDMPKFF KPRLGMTKEE MMIFIEASSE NPCSLYSSVC YSPQAEKVYK LCSPPADLHK VGTVVTPDND IYI AGGQVP LKNTKTNHSK TSKLQTAFRT VNCFYWFDAQ QNTWFPKTPM LFVRIKPSLV CCEGYIYAIG GDSVGGELNR RTVE RYDTE KDEWTMVSPL PCAWQWSAAV VVHDCIYVMT LNLMYCYFPR SDSWVEMAMR QTSRSFASAA AFGDKIFYIG GLHIA TNSG IRLPSGTVDG SSVTVEIYDV NKNEWKMAAN IPAKRYSDPC VRAVVISNSL CVFMRETHLN ERAKYVTYQY DLELDR WSL RQHISERVLW DLGRDFRCTV GKLYPSCLEE SPWKPPTYLF STDGTEEFEL DGEMVALPPV

UniProtKB: Kelch repeat and BTB domain-containing protein 2

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Macromolecule #3: Phosphatidylinositol 3-kinase regulatory subunit alpha

MacromoleculeName: Phosphatidylinositol 3-kinase regulatory subunit alpha
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.710281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAEGYQYRA LYDYKKEREE DIDLHLGDIL TVNKGSLVAL GFSDGQEARP EEIGWLNGYN ETTGERGDFP GTYVEYIGRK KISPPTPKP RPPRPLPVAP GSSKTEADVE QQALTLPDLA EQFAPPDIAP PLLIKLVEAI EKKGLECSTL YRTQSSSNLA E LRQLLDCD ...String:
MSAEGYQYRA LYDYKKEREE DIDLHLGDIL TVNKGSLVAL GFSDGQEARP EEIGWLNGYN ETTGERGDFP GTYVEYIGRK KISPPTPKP RPPRPLPVAP GSSKTEADVE QQALTLPDLA EQFAPPDIAP PLLIKLVEAI EKKGLECSTL YRTQSSSNLA E LRQLLDCD TPSVDLEMID VHVLADAFKR YLLDLPNPVI PAAVYSEMIS LAPEVQSSEE YIQLLKKLIR SPSIPHQYWL TL QYLLKHF FKLSQTSSKN LLNARVLSEI FSPMLFRFSA ASSDNTENLI KVIEILISTE WNERQPAPAL PPKPPKPTTV ANN GMNNNM SLQDAEWYWG DISREEVNEK LRDTADGTFL VRDASTKMHG DYTLTLRKGG NNKLIKIFHR DGKYGFSDPL TFSS VVELI NHYRNESLAQ YNPKLDVKLL YPVSKYQQDQ VVKEDNIEAV GKKLHEYNTQ FQEKSREYDR LYEEYTRTSQ EIQMK RTAI EAFNETIKIF EEQCQTQERY SKEYIEKFKR EGNEKEIQRI MHNYDKLKSR ISEIIDSRRR LEEDLKKQAA EYREID KRM NSIKPDLIQL RKTRDQYLMW LTQKGVRQKK LNEWLGNENT EDQYSLVEDD EDLPHHDEKT WNVGSSNRNK AENLLRG KR DGTFLVRESS KQGCYACSVV VDGEVKHCVI NKTATGYGFA EPYNLYSSLK ELVLHYQHTS LVQHNDSLNV TLAYPVYA Q QRR

UniProtKB: Phosphatidylinositol 3-kinase regulatory subunit alpha

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Macromolecule #4: Cullin-3

MacromoleculeName: Cullin-3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.063328 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM ...String:
MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM IARERKGEVV DRGAIRNACQ MLMILGLEGR SVYEEDFEAP FLEMSAEFFQ MESQKFLAEN SASVYIKKVE AR INEEIER VMHCLDKSTE EPIVKVVERE LISKHMKTIV EMENSGLVHM LKNGKTEDLG CMYKLFSRVP NGLKTMCECM SSY LREQGK ALVSEEGEGK NPVDYIQGLL DLKSRFDRFL LESFNNDRLF KQTIAGDFEY FLNLNSRSPE YLSLFIDDKL KKGV KGLTE QEVETILDKA MVLFRFMQEK DVFERYYKQH LARRLLTNKS VSDDSEKNMI SKLKTECGCQ FTSKLEGMFR DMSIS NTTM DEFRQHLQAT GVSLGGVDLT VRVLTTGYWP TQSATPKCNI PPAPRHAFEI FRRFYLAKHS GRQLTLQHHM GSADLN ATF YGPVKKEDGS EVGVGGAQVT GSNTRKHILQ VSTFQMTILM LFNNREKYTF EEIQQETDIP ERELVRALQS LACGKPT QR VLTKEPKSKE IENGHIFTVN DQFTSKLHRV KIQTVAAKQG ESDPERKETR QKVDDDRKHE IEAAIVRIMK SRKKMQHN V LVAEVTQQLK ARFLPSPVVI KKRIEGLIER EYLARTPEDR KVYTYVA

UniProtKB: Cullin-3

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ovu


Details: 7CIO
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 333476

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