mitochondrial matrix

GO:0005759 · Membrane organelle · Subcellular region · Proposed

The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. [GO:0005759]

Synonyms: mitochondrial lumen; mitochondrial stroma

Part of: mitochondrion (GO:0005739)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Taxonomic distribution

NCBITaxon:2759 Eukaryota — VARIABLE: Canonical mitochondrial matrices occur with canonical mitochondria in eukaryotes, while some anaerobic lineages carry reduced mitochondrion-related organelles instead. [GO:0005759]
NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding-yeast mitochondria contain matrix and membrane-associated mitochondrial proteins in purified mitochondrial proteomes. [DOI:10.1073/pnas.2135385100]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Budding-yeast model whose purified mitochondrial proteome includes matrix and membrane-associated mitochondrial machinery. [DOI:10.1073/pnas.2135385100]

Mechanism graphs

Mitochondrial matrix topology (FUNCTION)

The mitochondrial matrix is the mitochondrial lumen enclosed by the mitochondrial inner membrane.

Subject	Predicate	Object	Evidence
mitochondrial matrix	is part of	mitochondrion	`GO:0005759` GO:0005759 defines the matrix by its location in the matrix space, or lumen, of a mitochondrion. `GO:0005739` GO:0005739 identifies the containing mitochondrion.
mitochondrial inner membrane	encloses	mitochondrial matrix	`GO:0005759` GO:0005759 identifies the matrix as the mitochondrial matrix space or lumen. `GO:0005743` GO:0005743 defines the inner membrane as the lumen-facing mitochondrial-envelope bilayer.

Evidence

GO:0005759 Gene Ontology cellular-component term for mitochondrial matrix.
GO:0070013 Gene Ontology cellular-component parent term for intracellular organelle lumen.
GO:0005739 Gene Ontology cellular-component term for the mitochondrion that contains the matrix.
GO:0005743 Gene Ontology cellular-component term for the inner mitochondrial membrane that encloses the matrix.
DOI:10.1073/pnas.2135385100 Sickmann et al. 2003, 'The proteome of Saccharomyces cerevisiae mitochondria', Proceedings of the National Academy of Sciences.

Curation history

2026-09-14T00:48:59Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-14T00:49:32Z codex · EXPANDED_RECORD — Added GO parentage, mitochondrion parthood, GO synonyms, Eukaryota and Saccharomyces scope, GO/DOI evidence, and a nonmechanistic matrix-topology graph.

Source: data/structures/membrane_organelle/mitochondrial_matrix.yaml