Cryptochrome radical-pair photochemistry. Cryptochrome is the only plant entity in the review's bibliography where a magnetic field was applied and an effect measured on the protein's own chemistry rather than on a downstream phenotype, so it carries the atlas's only T1 annotations. The hyperfine partners that make this pair field-sensitive are the flavin's own nitrogens and protons — 14N at 99.6% natural abundance and 1H at essentially 100% — so unlike the 57Fe route argued for iron-sulfur clusters, this one is not abundance-limited. That asymmetry is much of why cryptochrome is the strongest case here and the Fe/S nodes elsewhere are not. Phytochrome B is drawn deliberately as context with no quantum claim: its photochemistry is a Z/E isomerisation offering no spin-based route, so reported field effects on phytochrome signalling are most simply a downstream consequence of cryptochrome. Note also that one blinded replication (Harris et al. 2009) did NOT reproduce cryptochrome-dependent field effects; that result is recorded in the ontology on the same footing as the positive reports. Derived from: Figure 3 panel A of Porterfield & Barker, "Plant Responses to Near-Null Magnetic Fields" — expanded to the photocycle and bound to Arabidopsis loci radical_pair_acceptor flavin_semiquinone triplet_yield_sensitive 1H 14N CHEBI:57692 AT4G08920 GO:0005634 Magnetic intensity affects cryptochrome-dependent responses in Arabidopsis thaliana. Theoretical analysis of Arabidopsis cryptochrome-1 shows magnetic fields could alter activation yields through radical-pair spin dynamics. Under blinded conditions, cryptochrome-dependent magnetic-field effects in Arabidopsis were NOT reproduced. Magnetic sensitivity mediated by Arabidopsis cryptochrome occurs during flavin reoxidation in the dark, not during photoreduction. Blue-light-dependent phosphorylation of cryptochromes is affected by magnetic fields in Arabidopsis. The reference case for the radical-pair mechanism in biology, and the entity from which the review's whole argument is generalised outward. Direction of effect is not consistent across the literature, and one blinded replication attempt failed (see Harris2009 below). Treat the magnitude as unsettled even though the mechanism is well characterised. radical_pair_acceptor flavin_semiquinone triplet_yield_sensitive 1H 14N CHEBI:57692 AT1G04400 GO:0005634 A near-null magnetic field affects cryptochrome-related hypocotyl growth and flowering in Arabidopsis. Geomagnetic field variation impacts cryptochrome and phytochrome signalling. Same FAD/tryptophan-triad chemistry as CRY1. CRY2's route to flowering time is the mechanistic link between the photoreceptor evidence and the most reproducible NNMF phenotype in the literature — delayed flowering. structural_context AT2G18790 flavin_semiquinone radical_pair_acceptor triplet_yield_sensitive 1H 14N CHEBI:57692 CHEBI:57692 The magnetically sensitive step is flavin reoxidation in the dark rather than photoreduction, implying a longer-lived radical pair than first assumed. The hyperfine partners that make this radical pair field-sensitive are the isoalloxazine ring's own nitrogens and protons — 14N at 99.6% abundance and 1H at essentially 100%. Unlike the 57Fe route argued for Fe/S clusters, this one is not abundance-limited, which is a large part of why cryptochrome is the strongest case in the atlas. radical_pair_donor hyperfine_coupled 1H 14N AT4G08920 AT1G04400 Spin dynamics of the FAD-tryptophan radical pair in Arabidopsis cryptochrome-1 can be modulated by an applied magnetic field. The donor half of the canonical pair. Its indole nitrogen and ring protons supply the hyperfine coupling on the donor side. triplet_yield_sensitive spin_correlated_pair hyperfine_coupled 1H 14N A photoreceptor-based radical-pair model can in principle transduce a geomagnetic-strength field into a change in signalling yield. Review of magnetic field effects in biology from the radical-pair perspective, covering the lifetime and hyperfine conditions required. This is the mechanism itself rather than a molecule. It is on the map because the review's argument is that this step, not the protein, is what generalises to other flavoproteins and Fe/S centres. For a field of geomagnetic magnitude to compete, the radical pair must live long enough for mixing to accumulate — roughly the microsecond scale. That lifetime requirement is what most candidate sites elsewhere in this atlas have not been shown to meet. structural_context structural_context Reduction of the geomagnetic field to below 100 nT delayed Arabidopsis flowering and downregulated flowering-related genes. Suppression of Arabidopsis flowering by a near-null magnetic field depends on the light conditions. Removal of the local geomagnetic field affected reproductive growth, including silique number and seed yield. cofactor_insertion cofactor_insertion electron_transfer direct_influence direct_influence direct_influence inhibition inhibition indirect_influence hormonal_feedback indirect_influence indirect_influence