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Yorodumi- PDB-8w4j: Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w4j | ||||||
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Title | Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / E3 ligase | ||||||
Function / homology | Function and homology information L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate biosynthetic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / polar microtubule / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate biosynthetic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / polar microtubule / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / cellular response to L-leucine / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / intercellular bridge / mitotic spindle assembly checkpoint signaling / glutamine metabolic process / protein monoubiquitination / mitotic sister chromatid segregation / ubiquitin-like ligase-substrate adaptor activity / NAD+ binding / positive regulation of TORC1 signaling / substantia nigra development / negative regulation of autophagy / 14-3-3 protein binding / ADP binding / cellular response to amino acid stimulus / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / mitotic spindle / microtubule cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||
Authors | Su, M.-Y. / Su, M.-Y. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w4j.cif.gz | 627.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w4j.ent.gz | 497.5 KB | Display | PDB format |
PDBx/mmJSON format | 8w4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/8w4j ftp://data.pdbj.org/pub/pdb/validation_reports/w4/8w4j | HTTPS FTP |
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-Related structure data
Related structure data | 37266MC 8kgyC 8khpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1900 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 1.072 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62817 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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