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- EMDB-61722: Structure of human IVD in complex with FAD and butyryl-CoA -

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Basic information

Entry
Database: EMDB / ID: EMD-61722
TitleStructure of human IVD in complex with FAD and butyryl-CoA
Map data
Sample
  • Complex: Homo tetramer of IVD in complex with FAD and butyryl-CoA
    • Protein or peptide: Isovaleryl-CoA dehydrogenase, mitochondrial
  • Ligand: Butyryl Coenzyme A
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsIVD / FAD / butyryl-CoA / HYDROLASE
Function / homology
Function and homology information


Isovaleric acidemia / isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / L-leucine catabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix ...Isovaleric acidemia / isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / L-leucine catabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
Isovaleryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsJu K / Xu Y / Bai F / Luan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902085 China
CitationJournal: Res
Title: Structural Insights into Isovaleryl-Coenzyme A Dehydrogenase: Mechanisms of Substrate Specificity and Implications of Isovaleric Acidemia-Associated Mutations
Authors: Ju K / Bai F / Xu Y / Li Q / Su G / Jin Y / Chen H / Zhang S / Luan X
History
DepositionSep 27, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_61722.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.0172458 - 3.175642
Average (Standard dev.)0.004869601 (±0.09993527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Homo tetramer of IVD in complex with FAD and butyryl-CoA

EntireName: Homo tetramer of IVD in complex with FAD and butyryl-CoA
Components
  • Complex: Homo tetramer of IVD in complex with FAD and butyryl-CoA
    • Protein or peptide: Isovaleryl-CoA dehydrogenase, mitochondrial
  • Ligand: Butyryl Coenzyme A
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Homo tetramer of IVD in complex with FAD and butyryl-CoA

SupramoleculeName: Homo tetramer of IVD in complex with FAD and butyryl-CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isovaleryl-CoA dehydrogenase, mitochondrial

MacromoleculeName: Isovaleryl-CoA dehydrogenase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: isovaleryl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.649668 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEMATATRL LGWRVASWRL RPPLAGFVSQ RAHSLLPVDD AINGLSEEQR QLRQTMAKFL QEHLAPKAQE IDRSNEFKNL REFWKQLGN LGVLGITAPV QYGGSGLGYL EHVLVMEEIS RASGAVGLSY GAHSNLCINQ LVRNGNEAQK EKYLPKLISG E YIGALAMS ...String:
MAEMATATRL LGWRVASWRL RPPLAGFVSQ RAHSLLPVDD AINGLSEEQR QLRQTMAKFL QEHLAPKAQE IDRSNEFKNL REFWKQLGN LGVLGITAPV QYGGSGLGYL EHVLVMEEIS RASGAVGLSY GAHSNLCINQ LVRNGNEAQK EKYLPKLISG E YIGALAMS EPNAGSDVVS MKLKAEKKGN HYILNGNKFW ITNGPDADVL IVYAKTDLAA VPASRGITAF IVEKGMPGFS TS KKLDKLG MRGSNTCELI FEDCKIPAAN ILGHENKGVY VLMSGLDLAR LVLAGGPLGL MQAVLDHTIP YLHVREAFGQ KIG HFQLMQ GKMADMYTRL MACRQYVYNV AKACDEGHCT AKDCAGVILY SAECATQVAL DGIQCFGGNG YINDFPMGRF LRDA KLYEI GAGTSEVRRL VIGRAFNADF H

UniProtKB: Isovaleryl-CoA dehydrogenase, mitochondrial

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Macromolecule #2: Butyryl Coenzyme A

MacromoleculeName: Butyryl Coenzyme A / type: ligand / ID: 2 / Number of copies: 4 / Formula: BCO
Molecular weightTheoretical: 837.624 Da
Chemical component information

ChemComp-BCO:
Butyryl Coenzyme A

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Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141942
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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