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- PDB-8w4j: Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamat... -

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Basic information

Entry
Database: PDB / ID: 8w4j
TitleCryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I
Components
  • Glutamate dehydrogenase 1, mitochondrial
  • Kelch-like protein 22
KeywordsSTRUCTURAL PROTEIN / E3 ligase
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / L-leucine binding / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / polar microtubule / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / L-glutamate catabolic process ...glutamate dehydrogenase [NAD(P)+] activity / L-leucine binding / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / polar microtubule / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / L-glutamate catabolic process / cellular response to L-leucine / positive regulation of T cell mediated immune response to tumor cell / glutamine metabolic process / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / NAD+ binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / intercellular bridge / 14-3-3 protein binding / positive regulation of TORC1 signaling / Mitochondrial protein degradation / substantia nigra development / negative regulation of autophagy / cellular response to amino acid stimulus / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / ADP binding / positive regulation of T cell activation / mitotic spindle / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / microtubule cytoskeleton / positive regulation of cell growth / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / mitochondrial matrix / cell division / intracellular membrane-bounded organelle / centrosome / GTP binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Kelch-like protein 22 / NAD(P) binding domain of glutamate dehydrogenase / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal ...Kelch-like protein 22 / NAD(P) binding domain of glutamate dehydrogenase / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glutamate dehydrogenase 1, mitochondrial / Kelch-like protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsSu, M.-Y. / Su, M.-Y.
Funding support1items
OrganizationGrant numberCountry
Other government2022A1515010856
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 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
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Revision 1.1Nov 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 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

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Assembly

Deposited unit
A: Glutamate dehydrogenase 1, mitochondrial
B: Glutamate dehydrogenase 1, mitochondrial
C: Glutamate dehydrogenase 1, mitochondrial
D: Glutamate dehydrogenase 1, mitochondrial
E: Glutamate dehydrogenase 1, mitochondrial
F: Glutamate dehydrogenase 1, mitochondrial
I: Kelch-like protein 22
J: Kelch-like protein 22


Theoretical massNumber of molelcules
Total (without water)512,3748
Polymers512,3748
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
Glutamate dehydrogenase 1, mitochondrial / GDH 1


Mass: 61480.746 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P00367, glutamate dehydrogenase [NAD(P)+]
#2: 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
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: the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I
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: 1.072 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62817 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327630
ELECTRON MICROSCOPYf_angle_d0.44837679
ELECTRON MICROSCOPYf_dihedral_angle_d3.3534296
ELECTRON MICROSCOPYf_chiral_restr0.0424412
ELECTRON MICROSCOPYf_plane_restr0.0045016

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