8SGV | pdb_00008sgv

human liver mitochondrial Catalase

PDB DOI: https://doi.org/10.2210/pdb8SGV/pdb
EM Map EMD-40469: 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: 2.58 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: 244.8 kDa
Atom Count: 16,409
Modeled Residue Count: 1,993
Deposited Residue Count: 2,108
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A [auth B], B [auth A], C, D	527	Homo sapiens	Mutation(s): 0 EC: 1.11.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P04040 (Homo sapiens) Explore P04040 Go to UniProtKB: P04040
PHAROS: P04040 GTEx: ENSG00000121691
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04040
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth B], H [auth A], J [auth C], L [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain F [auth B] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth B], G [auth A], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth D]