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- EMDB-60407: Structure of human ECHS1 in complex with Octanoyl-CoA -

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Basic information

Entry
Database: EMDB / ID: EMD-60407
TitleStructure of human ECHS1 in complex with Octanoyl-CoA
Map data
Sample
  • Complex: ECHS1
    • Protein or peptide: Enoyl-CoA hydratase, mitochondrial
  • Ligand: OCTANOYL-COENZYME A
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsECHS1 / Octanoyl-CoA / HYDROLASE
Function / homology
Function and homology information


Mitochondrial short-chain enoyl-CoA hydratase deficiency 1 / 3-hydroxypropionyl-CoA dehydratase activity / (2E)-butenoyl-CoA hydratase activity / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity ...Mitochondrial short-chain enoyl-CoA hydratase deficiency 1 / 3-hydroxypropionyl-CoA dehydratase activity / (2E)-butenoyl-CoA hydratase activity / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / enoyl-CoA hydratase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion
Similarity search - Function
Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsSu G / Xu Y / Chen B / Ju K / Sun X / Jin Y / Liu D / Chen H / Zhang S / Luan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902085 China
CitationJournal: Commun Biol / Year: 2025
Title: Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition.
Authors: Gengchen Su / Youwei Xu / Binxian Chen / Kaide Ju / Ye Jin / Houzao Chen / Shuyang Zhang / Xiaodong Luan /
Abstract: Deficiency of short-chain enoyl-CoA hydratase (ECHS1), a crucial enzyme in fatty acid metabolism through the mitochondrial β-oxidation pathway, has been strongly linked to various diseases, ...Deficiency of short-chain enoyl-CoA hydratase (ECHS1), a crucial enzyme in fatty acid metabolism through the mitochondrial β-oxidation pathway, has been strongly linked to various diseases, especially cardiomyopathy. However, the structural and biochemical mechanisms through which ECHS1 recognizes acyl-CoAs remain poorly understood. Herein, cryo-EM analysis reveals the apo structure of ECHS1 and structures of the ECHS1-crotonyl-CoA, ECHS1-acetoacetyl-CoA, ECHS1-hexanoyl-CoA, and ECHS1-octanoyl-CoA complexes at high resolutions. The mechanism through which ECHS1 recognizes its substrates varies with the fatty acid chain lengths of acyl-CoAs. Furthermore, crucial point mutations in ECHS1 have a great impact on substrate recognition, resulting in significant changes in binding affinity and enzyme activity, as do disease-related point mutations in ECHS1. The functional mechanism of ECHS1 is systematically elucidated from structural and biochemical perspectives. These findings provide a theoretical basis for subsequent work focused on determining the role of ECHS1 deficiency (ECHS1D) in the occurrence of diseases such as cardiomyopathy.
History
DepositionJun 5, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60407.png

Downloads & links

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Map

FileDownload / File: emd_60407.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.53
Minimum - Maximum-2.3287325 - 3.7722545
Average (Standard dev.)0.00028238868 (±0.13727205)
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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Half map: #2

Fileemd_60407_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60407_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : ECHS1

EntireName: ECHS1
Components
  • Complex: ECHS1
    • Protein or peptide: Enoyl-CoA hydratase, mitochondrial
  • Ligand: OCTANOYL-COENZYME A
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: ECHS1

SupramoleculeName: ECHS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Enoyl-CoA hydratase, mitochondrial

MacromoleculeName: Enoyl-CoA hydratase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: enoyl-CoA hydratase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.3756 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: ASGANFEYII AEKRGKNNTV GLIQLNRPKA LNALCDGLID ELNQALKTFE EDPAVGAIVL TGGDKAFAAG ADIKEMQNLS FQDCYSSKF LKHWDHLTQV KKPVIAAVNG YAFGGGCELA MMCDIIYAGE KAQFAQPEIL IGTIPGAGGT QRLTRAVGKS L AMEMVLTG ...String:
ASGANFEYII AEKRGKNNTV GLIQLNRPKA LNALCDGLID ELNQALKTFE EDPAVGAIVL TGGDKAFAAG ADIKEMQNLS FQDCYSSKF LKHWDHLTQV KKPVIAAVNG YAFGGGCELA MMCDIIYAGE KAQFAQPEIL IGTIPGAGGT QRLTRAVGKS L AMEMVLTG DRISAQDAKQ AGLVSKICPV ETLVEEAIQC AEKIASNSKI VVAMAKESVN AAFEMTLTEG SKLEKKLFYS TF ATDDRKE GMTAFVEKRK ANFKDQ

UniProtKB: Enoyl-CoA hydratase, mitochondrial

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Macromolecule #2: OCTANOYL-COENZYME A

MacromoleculeName: OCTANOYL-COENZYME A / type: ligand / ID: 2 / Number of copies: 6 / Formula: CO8
Molecular weightTheoretical: 893.73 Da
Chemical component information

ChemComp-CO8:
OCTANOYL-COENZYME A

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133705
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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