nucleus

GO:0005634 · Membrane organelle · Membrane bounded organelle · Proposed

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. [GO:0005634]

Synonyms: cell nucleus

Has part: nuclear envelope (GO:0005635); nuclear lumen (GO:0031981); nuclear pore (GO:0005643)

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

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
nuclear pore	Protein complex	part of	`GO:0005643`			UNKNOWN	Membrane-embedded pore complex that spans the nuclear envelope and mediates exchange between nucleoplasm and cytoplasm. `GO:0005643` GO:0005643 defines the nuclear pore as a protein complex that provides a discrete opening in the nuclear envelope.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding-yeast nuclei can contact the vacuole at nucleus-vacuole junctions formed by direct Vac8p-Nvj1p interaction. [DOI:10.1091/mbc.11.7.2445]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Budding-yeast example in which the nucleus can form direct nucleus-vacuole junctions with the vacuole. [DOI:10.1091/mbc.11.7.2445]

Functions

genome compartmentalization — The nucleus encloses the nuclear lumen where nuclear chromosomes are housed and replicated.
- GO:0005634 GO:0005634 defines the nucleus as the membrane-bounded organelle in which chromosomes are housed and replicated.
nucleocytoplasmic transport GO:0006913 — Nuclear pores embedded in the envelope provide gated exchange between the nuclear lumen and cytoplasm.
- GO:0005643 GO:0005643 defines nuclear pores as openings in the nuclear envelope.
- DOI:10.1534/genetics.111.127803 Aitchison and Rout 2012 review budding-yeast NPC organization and transport.

Mechanism graphs

Nuclear envelope bounds a pore-gated lumen (FUNCTION)

In budding yeast, the nuclear envelope surrounds the nuclear lumen and is perforated by nuclear pores that mediate nucleocytoplasmic exchange.

Subject	Predicate	Object	Evidence
nuclear envelope	bounds	nuclear lumen	`GO:0031981` GO:0031981 defines the nuclear lumen as the volume enclosed by the nuclear inner membrane.
nuclear envelope	encloses	nucleus	`GO:0005635` GO:0005635 defines the nuclear envelope as the double lipid bilayer that encloses the nucleus.
nuclear pore	spans	nuclear envelope	`GO:0005643` GO:0005643 places nuclear pores at openings in the nuclear envelope where the inner and outer nuclear membranes are joined.
nuclear pore	mediates	nucleocytoplasmic transport	`DOI:10.1534/genetics.111.127803` Aitchison and Rout 2012 review transport through the budding-yeast nuclear pore complex.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral boundaries and groundings for chromatin, nucleolar RNP, and nuclear-envelope-associated protein cohorts in the nucleus. This first nucleus record grounds the nuclear pore as an exact protein-complex component but avoids treating chromatin or nucleolar cohorts as a single exact protein, RNA, or DNA component.

Evidence

GO:0005634 Gene Ontology cellular-component term for nucleus.
GO:0005635 Gene Ontology cellular-component term for nuclear envelope.
GO:0031981 Gene Ontology cellular-component term for nuclear lumen.
GO:0005643 Gene Ontology cellular-component term for nuclear pore.
DOI:10.1091/mbc.11.7.2445 Pan et al. 2000, 'Nucleus-vacuole junctions in Saccharomyces cerevisiae are formed through the direct interaction of Vac8p with Nvj1p', Molecular Biology of the Cell.
DOI:10.1080/21541248.2021.1993714 Luo et al. 2022, 'Unexplored Cdc42 functions at the budding yeast nucleus suggested by subcellular localization', Small GTPases.
DOI:10.1534/genetics.111.127803 Aitchison and Rout 2012, 'The Yeast Nuclear Pore Complex and Transport Through It', Genetics.

Curation history

2026-09-11T17:34:12Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-11T17:35:06Z codex · EXPANDED_RECORD — Added nucleus parentage, nuclear envelope, nuclear lumen, and nuclear pore parts, exact synonymy, a grounded nuclear pore component, Saccharomyces scope, genome-compartmentalization and transport functions, a nonmechanistic envelope-and-pore graph, and a nuclear-component grounding TODO.
2026-09-11T17:43:08Z codex · REVIEW_FIXES — Retyped the GO:0005643 nuclear-pore graph node as a structure and narrowed budding-yeast taxon/example notes to the cited nucleus-vacuole-junction evidence.

Source: data/structures/membrane_organelle/nucleus.yaml