8ZRW | pdb_00008zrw

Structure of human ECHS1 in complex with Octanoyl-CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition.

Su, G.Xu, Y.Chen, B.Ju, K.Jin, Y.Chen, H.Zhang, S.Luan, X.

(2025) Commun Biol 8: 619-619

  • DOI: https://doi.org/10.1038/s42003-025-07924-0
  • Primary Citation of Related Structures:  
    8ZRU, 8ZRV, 8ZRW, 8ZRX, 8ZRY

  • PubMed 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, 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.


  • Organizational Affiliation

    Department of Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, 100730, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase, mitochondrial
A, B, C, D, E
A, B, C, D, E, F
263Homo sapiensMutation(s): 0 
Gene Names: ECHS1
EC: 4.2.1.17 (PDB Primary Data), 5.3.3.8 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P30084 (Homo sapiens)
Explore P30084 
Go to UniProtKB:  P30084
PHAROS:  P30084
GTEx:  ENSG00000127884 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30084
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO8 (Subject of Investigation/LOI)
Query on CO8

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
J [auth C]
K [auth D]
L [auth E]
G [auth A],
I [auth B],
J [auth C],
K [auth D],
L [auth E],
N [auth F]
OCTANOYL-COENZYME A
C29 H50 N7 O17 P3 S
KQMZYOXOBSXMII-CECATXLMSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
M [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81902085

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release