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- PDB-9jq4: Structure of human IVD in complex with FAD and butyryl-CoA -

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Basic information

Entry
Database: PDB / ID: 9jq4
TitleStructure of human IVD in complex with FAD and butyryl-CoA
ComponentsIsovaleryl-CoA dehydrogenase, mitochondrial
KeywordsHYDROLASE / IVD / FAD / butyryl-CoA
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
Butyryl Coenzyme A / FLAVIN-ADENINE DINUCLEOTIDE / Isovaleryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsJu, K. / Xu, Y. / Bai, F. / Luan, X.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isovaleryl-CoA dehydrogenase, mitochondrial
B: Isovaleryl-CoA dehydrogenase, mitochondrial
C: Isovaleryl-CoA dehydrogenase, mitochondrial
D: Isovaleryl-CoA dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,09112
Polymers186,5994
Non-polymers6,4938
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
Isovaleryl-CoA dehydrogenase, mitochondrial / IVD / Butyryl-CoA dehydrogenase


Mass: 46649.668 Da / Num. of mol.: 4 / Mutation: E286A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IVD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P26440, isovaleryl-CoA dehydrogenase, short-chain acyl-CoA dehydrogenase
#2: Chemical
ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Has ligand of interestN
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: Homo tetramer of IVD in complex with FAD and butyryl-CoA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141942 / Symmetry type: POINT

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