chloroplast thylakoid lumen

GO:0009543 · Membrane organelle · Subcellular region · Proposed

The volume enclosed by the membrane of a chloroplast thylakoid. [GO:0009543]

Part of: chloroplast thylakoid (GO:0009534)

Xrefs: uniprot.location:SL-0057 — Chloroplast thylakoid lumen

Taxonomic distribution

NCBITaxon:33090 Viridiplantae — COMMON: Green algae and land plants with internal chloroplast thylakoid membranes have a lumenal compartment inside those membranes. [DOI:10.1146/annurev-cellbio-120823-022747]
NCBITaxon:3055 Chlamydomonas reinhardtii — COMMON: Native Chlamydomonas chloroplast thylakoids include a lumenal compartment inside stacked and unstacked thylakoid membrane regions. [DOI:10.7554/eLife.04889]

NCBITaxon:3055 Chlamydomonas reinhardtii — Unicellular green alga used for in situ cryo-electron tomography of native chloroplast thylakoid lumen and membrane architecture. [DOI:10.7554/eLife.04889]

The chloroplast thylakoid lumen is the internal chloroplast thylakoid compartment enclosed by the thylakoid membrane.

Subject	Predicate	Object	Evidence
chloroplast thylakoid membrane	encloses	chloroplast thylakoid lumen	`GO:0009543` GO:0009543 defines the chloroplast thylakoid lumen as the volume enclosed by a chloroplast thylakoid membrane. `uniprot.location:SL-0057` — Chloroplast thylakoid lumen UniProt SL-0057 describes the chloroplast thylakoid lumen as a chloroplast thylakoid child compartment. `GO:0009535` GO:0009535 identifies the chloroplast thylakoid membrane enclosing the lumen. `uniprot.location:SL-0058` — Chloroplast thylakoid membrane UniProt SL-0058 maps the chloroplast thylakoid membrane to GO:0009535 and places it under chloroplast thylakoid.

INTERPRETATION (RESOLVED): Keep the chloroplast thylakoid membrane as the boundary of the chloroplast thylakoid lumen rather than as a lumen component. GO:0009543 denotes the volume enclosed by a chloroplast thylakoid membrane, whereas GO:0009535 denotes the pigmented membrane that encloses that volume.

GO:0009543 Gene Ontology cellular-component term for chloroplast thylakoid lumen.
GO:0031978 Gene Ontology cellular-component term for plastid thylakoid lumen, the broader plastid thylakoid-lumen parent.
GO:0009534 Gene Ontology cellular-component term for the chloroplast thylakoid that this lumen is part of.
GO:0009535 Gene Ontology cellular-component term for the chloroplast thylakoid membrane that encloses this lumen.
uniprot.location:SL-0057 — Chloroplast thylakoid lumen UniProt Subcellular Location SL-0057 maps Chloroplast thylakoid lumen to GO:0009543 and places it under chloroplast thylakoid.
uniprot.location:SL-0058 — Chloroplast thylakoid membrane UniProt Subcellular Location SL-0058 maps the bounding chloroplast thylakoid membrane to GO:0009535.
DOI:10.1146/annurev-cellbio-120823-022747 Perez-Boerema et al. 2024, Evolution of Thylakoid Structural Diversity, Annual Review of Cell and Developmental Biology.
DOI:10.7554/eLife.04889 Engel et al. 2015, Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography, eLife.

2026-09-13T02:31:30Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-13T02:31:58Z codex · EXPANDED_RECORD — Added plastid thylakoid-lumen parentage, chloroplast thylakoid parthood, the UniProt SL-0057 xref, Viridiplantae and Chlamydomonas scope, literature and GO evidence, a nonmechanistic lumen-boundary topology graph, and a resolved boundary interpretation.
2026-09-13T02:37:27Z codex · ADDRESS_REVIEW — Resolved #740 by adding direct GO:0009535 and SL-0058 membrane evidence to the lumen-boundary topology edge and the boundary interpretation.