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- PDB-8khp: CULLIN3-KLHL22-RBX1 E3 ligase -

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Basic information

Entry
Database: PDB / ID: 8khp
TitleCULLIN3-KLHL22-RBX1 E3 ligase
Components
  • Cullin-3
  • E3 ubiquitin-protein ligase RBX1
  • Kelch-like protein 22
KeywordsSTRUCTURAL PROTEIN / E3 ligase
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / cullin-RING-type E3 NEDD8 transferase ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cellular response to L-leucine / cullin-RING ubiquitin ligase complex / RHOBTB3 ATPase cycle / positive regulation of T cell mediated immune response to tumor cell / positive regulation of mitotic metaphase/anaphase transition / embryonic cleavage / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cell projection organization / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / Notch binding / NEDD8 ligase activity / fibroblast apoptotic process / RHOBTB1 GTPase cycle / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / stem cell division / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / stress fiber assembly / mitotic spindle assembly checkpoint signaling / ubiquitin ligase complex scaffold activity / negative regulation of Rho protein signal transduction / negative regulation of mitophagy / Prolactin receptor signaling / positive regulation of cytokinesis / cullin family protein binding / mitotic sister chromatid segregation / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / sperm flagellum / RHOBTB2 GTPase cycle / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / intercellular bridge / gastrulation / 14-3-3 protein binding / transcription-coupled nucleotide-excision repair / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / negative regulation of autophagy / cyclin binding / Regulation of BACH1 activity / T cell activation / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / kidney development / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / protein destabilization / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of T cell activation / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex
Similarity search - Function
Kelch-like protein 22 / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / BTB-kelch protein / : / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch ...Kelch-like protein 22 / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / BTB-kelch protein / : / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Kelch motif / Kelch / Kelch repeat type 1 / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsSu, M.-Y. / Su, M.-Y.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.0Dec 13, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 13, 2023Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 13, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 13, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 13, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 22
B: Kelch-like protein 22
C: Cullin-3
D: Cullin-3
E: E3 ubiquitin-protein ligase RBX1
F: E3 ubiquitin-protein ligase RBX1


Theoretical massNumber of molelcules
Total (without water)346,1966
Polymers346,1966
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Kelch-like protein 22


Mass: 71744.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL22 / Production host: Homo sapiens (human) / References: UniProt: Q53GT1
#2: Protein Cullin-3 / CUL-3


Mass: 89063.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Homo sapiens (human) / References: UniProt: Q13618
#3: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Homo sapiens (human)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
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: CULLIN3-KLHL22-RBX1 E3 ligase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 1.07 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181834 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217807
ELECTRON MICROSCOPYf_angle_d0.46524295
ELECTRON MICROSCOPYf_dihedral_angle_d3.0812836
ELECTRON MICROSCOPYf_chiral_restr0.042970
ELECTRON MICROSCOPYf_plane_restr0.0023282

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