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- EMDB-37247: CULLIN3-KLHL22-RBX1 E3 ligase -

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Basic information

Entry
Database: EMDB / ID: EMD-37247
TitleCULLIN3-KLHL22-RBX1 E3 ligase
Map data
Sample
  • Complex: CULLIN3-KLHL22-RBX1 E3 ligase
    • Protein or peptide: Kelch-like protein 22
    • Protein or peptide: Cullin-3
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
KeywordsE3 ligase / STRUCTURAL PROTEIN
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / POZ domain binding / regulation protein catabolic process at postsynapse / negative regulation of Rho protein signal transduction / embryonic cleavage / polar microtubule / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / COPII vesicle coat assembly / positive regulation of protein K63-linked ubiquitination ...positive regulation of mitotic cell cycle phase transition / POZ domain binding / regulation protein catabolic process at postsynapse / negative regulation of Rho protein signal transduction / embryonic cleavage / polar microtubule / anaphase-promoting complex-dependent catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / COPII vesicle coat assembly / positive regulation of protein K63-linked ubiquitination / cellular response to L-leucine / RHOBTB3 ATPase cycle / negative regulation of beige fat cell differentiation / positive regulation of T cell mediated immune response to tumor cell / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / stem cell division / negative regulation of mitophagy / positive regulation of cilium assembly / cullin-RING ubiquitin ligase complex / regulation of xenophagy / positive regulation of mitotic metaphase/anaphase transition / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / Notch binding / establishment of endothelial barrier / positive regulation of protein autoubiquitination / protein neddylation / stress fiber assembly / regulation of BMP signaling pathway / NEDD8 ligase activity / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / RHOBTB1 GTPase cycle / protein K27-linked ubiquitination / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of TOR signaling / mitotic spindle assembly checkpoint signaling / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / intercellular bridge / Cul3-RING ubiquitin ligase complex / regulation of mitotic cytokinesis / regulation of DNA damage checkpoint / negative regulation of type I interferon production / positive regulation of cytokinesis / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / regulation of cell cycle phase transition / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / mitotic sister chromatid segregation / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / regulation of cellular response to stress / limb development / protein monoubiquitination / cullin family protein binding / mitotic metaphase chromosome alignment / endoplasmic reticulum to Golgi vesicle-mediated transport / RHOBTB2 GTPase cycle / centrosome duplication / regulation of DNA-templated DNA replication initiation / sperm flagellum / cilium assembly / protein autoubiquitination / ubiquitin-like ligase-substrate adaptor activity / kidney development / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / 14-3-3 protein binding / protein K48-linked ubiquitination / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / post-translational protein modification / gene expression / integrin-mediated signaling pathway / regulation of embryonic development / negative regulation of autophagy / cyclin binding / cellular response to amino acid stimulus / replication fork processing / positive regulation of protein ubiquitination
Similarity search - Function
Kelch-like protein 22 / KLHDC2/KLHL20/DRC7 Kelch-repeats 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 / Kelch / Kelch motif ...Kelch-like protein 22 / KLHDC2/KLHL20/DRC7 Kelch-repeats 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 / Kelch / Kelch motif / Kelch repeat type 1 / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / Kelch-type beta propeller / 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 / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-3 / Kelch-like protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsSu M-Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2022A1515010856 China
CitationJournal: Structure / Year: 2023
Title: Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme.
Authors: Fei Teng / Yang Wang / Ming Liu / Shuyun Tian / Goran Stjepanovic / Ming-Yuan Su /
Abstract: CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric ...CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric BTB-Kelch family proteins combine adapter and substrate receptor into a single polypeptide for the CULLIN3 family. However, the entire structural assembly and molecular details have not been elucidated to date. Here, we present a cryo-EM structure of the CULLIN3 in complex with Kelch-like protein 22 (KLHL22) and a mitochondrial glutamate dehydrogenase complex I (GDH1) at 3.06 Å resolution. The structure adopts a W-shaped architecture formed by E3 ligase dimers. Three CULLIN3 dimers were found to be dynamically associated with a single GDH1 hexamer. CULLIN3 ligase mediated the polyubiquitination of GDH1 in vitro. Together, these results enabled the establishment of a structural model for understanding the complete assembly of BTB-Kelch proteins with CULLIN3 and how together they recognize oligomeric substrates and target them for ubiquitination.
History
DepositionAug 22, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37247.png

Downloads & links

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Map

FileDownload / File: emd_37247.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.33801886 - 1.084867
Average (Standard dev.)0.0031075622 (±0.029384159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_37247_additional_1.map
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Half map: #2

Fileemd_37247_half_map_1.map
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Half map: #1

Fileemd_37247_half_map_2.map
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Sample components

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Entire : CULLIN3-KLHL22-RBX1 E3 ligase

EntireName: CULLIN3-KLHL22-RBX1 E3 ligase
Components
  • Complex: CULLIN3-KLHL22-RBX1 E3 ligase
    • Protein or peptide: Kelch-like protein 22
    • Protein or peptide: Cullin-3
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1

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Supramolecule #1: CULLIN3-KLHL22-RBX1 E3 ligase

SupramoleculeName: CULLIN3-KLHL22-RBX1 E3 ligase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Kelch-like protein 22

MacromoleculeName: Kelch-like protein 22 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.744594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEEQEFTQL CKLPAQPSHP HCVNNTYRSA QHSQALLRGL LALRDSGILF DVVLVVEGRH IEAHRILLAA SCDYFRGMFA GGLKEMEQE EVLIHGVSYN AMCQILHFIY TSELELSLSN VQETLVAACQ LQIPEIIHFC CDFLMSWVDE ENILDVYRLA E LFDLSRLT ...String:
MAEEQEFTQL CKLPAQPSHP HCVNNTYRSA QHSQALLRGL LALRDSGILF DVVLVVEGRH IEAHRILLAA SCDYFRGMFA GGLKEMEQE EVLIHGVSYN AMCQILHFIY TSELELSLSN VQETLVAACQ LQIPEIIHFC CDFLMSWVDE ENILDVYRLA E LFDLSRLT EQLDTYILKN FVAFSRTDKY RQLPLEKVYS LLSSNRLEVS CETEVYEGAL LYHYSLEQVQ ADQISLHEPP KL LETVRFP LMEAEVLQRL HDKLDPSPLR DTVASALMYH RNESLQPSLQ SPQTELRSDF QCVVGFGGIH STPSTVLSDQ AKY LNPLLG EWKHFTASLA PRMSNQGIAV LNNFVYLIGG DNNVQGFRAE SRCWRYDPRH NRWFQIQSLQ QEHADLSVCV VGRY IYAVA GRDYHNDLNA VERYDPATNS WAYVAPLKRE VYAHAGATLE GKMYITCGRR GEDYLKETHC YDPGSNTWHT LADGP VRRA WHGMATLLNK LYVIGGSNND AGYRRDVHQV ACYSCTSGQW SSVCPLPAGH GEPGIAVLDN RIYVLGGRSH NRGSRT GYV HIYDVEKDCW EEGPQLDNSI SGLAACVLTL PRSLLLEPPR GTPDRSQADP DFASEVMSVS DWEEFDNSSE D

UniProtKB: Kelch-like protein 22

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Macromolecule #2: Cullin-3

MacromoleculeName: Cullin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.063328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 #3: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 3 / 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: Homo sapiens (human)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181834
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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