8SGS | pdb_00008sgs

human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb8SGS/pdb
EM Map EMD-40466: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2023-04-13 Released: 2024-02-21
Deposition Author(s): Zhang, Z.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology.

Zhang, Z., Tringides, M.L., Morgan, C.E., Miyagi, M., Mears, J.A., Hoppel, C.L., Yu, E.W.

(2023) Mol Cell Proteomics 22: 100666-100666

PubMed: 37839702 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.mcpro.2023.100666
Primary Citation Related Structures:
8SGP, 8SGR, 8SGS, 8SGV, 8SHS, 8SK6, 8SK8, 8SKR, 8SKS

PubMed Abstract:
The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.

Organizational Affiliation

Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.

Macromolecule Content

Total Structure Weight: 183.6 kDa
Atom Count: 11,720
Modeled Residue Count: 1,524
Deposited Residue Count: 1,648
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain specific acyl-CoA dehydrogenase, mitochondrial	A, B, C, D	412	Homo sapiens	Mutation(s): 0 EC: 1.3.8.1
UniProt & NIH Common Fund Data Resources
Find proteins for P16219 (Homo sapiens) Explore P16219 Go to UniProtKB: P16219
PHAROS: P16219 GTEx: ENSG00000122971
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16219
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]