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- EMDB-37266: Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamat... -

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Basic information

Entry
Database: EMDB / ID: EMD-37266
TitleCryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I
Map data
Sample
  • Complex: the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
    • Protein or peptide: Kelch-like protein 22
KeywordsE3 ligase / STRUCTURAL PROTEIN
Function / homology
Function and homology information


L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / polar microtubule / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / glutamate dehydrogenase (NAD+) activity ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / polar microtubule / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / glutamate dehydrogenase (NAD+) activity / positive regulation of T cell mediated immune response to tumor cell / cellular response to L-leucine / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / intercellular bridge / glutamine metabolic process / mitotic spindle assembly checkpoint signaling / protein monoubiquitination / mitotic sister chromatid segregation / NAD+ binding / ubiquitin-like ligase-substrate adaptor activity / 14-3-3 protein binding / Mitochondrial protein degradation / substantia nigra development / positive regulation of TORC1 signaling / negative regulation of autophagy / cellular response to amino acid stimulus / ADP binding / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / mitotic spindle / microtubule cytoskeleton / positive regulation of T cell activation / 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
Kelch-like protein 22 / Kelch motif / Galactose oxidase, central domain / NAD(P) binding domain of glutamate dehydrogenase / 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 ...Kelch-like protein 22 / Kelch motif / Galactose oxidase, central domain / NAD(P) binding domain of glutamate dehydrogenase / 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 / Kelch motif / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsSu M-Y
Funding support1 items
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, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37266.png

Downloads & links

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Map

FileDownload / File: emd_37266.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-0.4727379 - 1.5896524
Average (Standard dev.)0.003634181 (±0.045847222)
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_37266_additional_1.map
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Half map: #2

Fileemd_37266_half_map_1.map
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Half map: #1

Fileemd_37266_half_map_2.map
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Sample components

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Entire : the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I

EntireName: the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I
Components
  • Complex: the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
    • Protein or peptide: Kelch-like protein 22

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Supramolecule #1: the CULLIN3-KLHL22-RBX1 E3 ligase bound to glutamate dehydrogenase I

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

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Macromolecule #1: Glutamate dehydrogenase 1, mitochondrial

MacromoleculeName: Glutamate dehydrogenase 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: glutamate dehydrogenase [NAD(P)+]
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.480746 KDa
SequenceString: MYRYLGEALL LSRAGPAALG SASADSAALL GWARGQPAAA PQPGLALAAR RHYSEAVADR EDDPNFFKMV EGFFDRGASI VEDKLVEDL RTRESEEQKR NRVRGILRII KPCNHVLSLS FPIRRDDGSW EVIEGYRAQH SQHRTPCKGG IRYSTDVSVD E VKALASLM ...String:
MYRYLGEALL LSRAGPAALG SASADSAALL GWARGQPAAA PQPGLALAAR RHYSEAVADR EDDPNFFKMV EGFFDRGASI VEDKLVEDL RTRESEEQKR NRVRGILRII KPCNHVLSLS FPIRRDDGSW EVIEGYRAQH SQHRTPCKGG IRYSTDVSVD E VKALASLM TYKCAVVDVP FGGAKAGVKI NPKNYTDNEL EKITRRFTME LAKKGFIGPG IDVPAPDMST GEREMSWIAD TY ASTIGHY DINAHACVTG KPISQGGIHG RISATGRGVF HGIENFINEA SYMSILGMTP GFGDKTFVVQ GFGNVGLHSM RYL HRFGAK CIAVGESDGS IWNPDGIDPK ELEDFKLQHG SILGFPKAKP YEGSILEADC DILIPAASEK QLTKSNAPRV KAKI IAEGA NGPTTPEADK IFLERNIMVI PDLYLNAGGV TVSYFEWLKN LNHVSYGRLT FKYERDSNYH LLMSVQESLE RKFGK HGGT IPIVPTAEFQ DRISGASEKD IVHSGLAYTM ERSARQIMRT AMKYNLGLDL RTAAYVNAIE KVFKVYNEAG VTFT

UniProtKB: Glutamate dehydrogenase 1, mitochondrial

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Macromolecule #2: Kelch-like protein 22

MacromoleculeName: Kelch-like protein 22 / type: protein_or_peptide / ID: 2 / 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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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: 1.072 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62817
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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