Photoreceptor that mediates primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, and regulates other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception. Photoexcited cryptochromes interact with signaling partner proteins to alter gene expression at both transcriptional and post-translational levels and, consequently, regulate the corresponding metabolic and developmental programs (PubMed:21841916). Blue-light absorbing flavoprotein that activates reversible flavin photoreduction via an electron transport chain comprising a tryptophan triad (W-324, W-377 and W-400), accompanied by a large conformational change upon photoexcitation, or via an alternative electron transport that involves small metabolites, including NADPH, NADH, and ATP. The half-life of the activated signaling state is about 5 minutes (PubMed:26313597, PubMed:25157750, PubMed:23398192, PubMed:21875594, PubMed:21467031). Also involved in the detection of blue/green ratio in light (shade under leaf canopies) and subsequent adaptations on plant growth and development (PubMed:20668058). In darkness, the dark reoxidation of flavin occurs and leads to inactivated state (PubMed:21467031, PubMed:23398192). Perceives low blue light (LBL) and responds by directly contacting two bHLH transcription factors, PIF4 and PIF5, at chromatin on E-box variant 5'-CA[CT]GTG-3' to promote their activity and stimulate specific gene expression to adapt global physiology (e.g. hypocotyl elongation and hyponastic growth in low blue light) (PubMed:26724867, PubMed:19558423). When activated by high-intensity blue light, catalyzes direct enzymatic conversion of molecular oxygen O(2) to reactive oxygen species (ROS) and hydrogen peroxide H(2)O(2) in vitro. ROS accumulation upon activation by blue light leads to cell death in protoplasts (PubMed:25728686). Seems essential for blue-light-triggered and singlet oxygen-mediated programmed cell death (PCD) (PubMed:17075038). Required for the induction of nuclear genes encoding photoprotective components by GATA24 and GATA28 in extreme light intensities that exceed the electron utilization capacity of the chloroplast (PubMed:22786870). Involved in shortening the circadian clock period, especially at 27 degrees Celsius, in blue light (BL) and required to maintain clock genes expression rhythm (PubMed:23511208). Mediates blue light-induced gene expression and hypocotyl elongation through the inhibition of COP1-mediated degradation of the transcription factors BIT1 and HY5 and via the activation of anion channels at the plasma membrane, probably via auxin signaling (PubMed:21511872, PubMed:21511871, PubMed:16093319, PubMed:18397371, PubMed:12324610, PubMed:8528277, PubMed:9765547, PubMed:25721730). Required for the hypocotyl hook formation in darkness (PubMed:22855128). Involved in blue light-dependent stomatal opening, CHS gene expression, transpiration, inhibition of stem growth and increase of root growth, probably by regulating abscisic acid (ABA) (PubMed:22147516, PubMed:16093319, PubMed:16703358, PubMed:7756321, PubMed:9565033). Prevents lateral roots growth by inhibiting auxin transport (PubMed:20133010). Necessary for shade avoidance syndrome (SAS), characterized by leaf hyponasty and reduced lamina/petiole ratio, when exposed to blue light attenuation (PubMed:21457375). Together with phototropins, involved in phototropism regulation by various blue light fluence; blue light attenuates phototropism in high fluence rates (100 umol.m-2.s-1) but enhances phototropism in low fluence rates (<1.0 umol.m-2.s-1) (PubMed:12857830). Required for blue/UV-A wavelengths-mediated inhibition of explants shoot regeneration in vitro (e.g. new shoot apical meristems regeneration from excised cotyledons) (PubMed:22681544). Modulates anthocyanin accumulation in a PHYA-dependent manner in far-red-light. Acts as a PHYA/PHYB-dependent modulator of chlorophyll accumulation in red light. Contributes to most blue light deetiolation responses (PubMed:9733523, PubMed:8528277). May act as a chemical magnetoreceptor, via magnetically sensitive kinetics and quantum yields of photo-induced flavin / tryptophan radical pairs (PubMed:22421133). The effect of near-null magnetic field on flowering is altered by changes of blue light cycle and intensity in a CRY1/CRY2-dependent manner (PubMed:26095447). Involved in the strigolactone signaling that regulates hypocotyl growth in response to blue light (PubMed:24126495). Modulates temperature-dependent growth and physiology maintenance, especially at warm ambient temperatures, via HFR1-dependent activity (PubMed:21265897). Implicated in promoting R protein-mediated resistance to Pseudomonas syringae pv. tomato (Pst.) DC3000 under continuous light conditions. Promotes systemic acquired resistance (SAR) and PR gene expression triggered by P. syringae. Binds 1 FAD per subunit. Binds 1 5,10-methenyltetrahydrofolate (MTHF) per subunit. Light exposure induces a conformational change in the C-terminal domain CCT1 required for activity. Homodimer. Interacts with ADO1, COP1 and PHYA. Interacts specifically with the dark/far-red (Pr) state of PHYB, but not with the red light-activated (Pfr) (PubMed:22577138). Interacts with PIF4 and PIF5 in the nucleus in response to low blue light (LBL) (PubMed:26724867). Binds to SPA1 and SPA4 in response to blue light, this interaction prevents SPA1/COP1 complex formation and thus avoid COP1-dependent degradation of the transcription factor HY5 by the proteasome and promotes hypocotyl elongation (PubMed:21511872, PubMed:21511871). Interacts with TCP2 (PubMed:26596765). Binding to ATP mediates conformational changes which facilitate flavin binding (PubMed:19327354, PubMed:17073458). The nuclear pool is involved in hypocotyl and petiole growth inhibition and anthocyanin production, while the cytoplasmic pool is involved in root growth and cotyledon expansion (PubMed:18003924). Present in nuclear bodies (NBs) (PubMed:21511872, PubMed:21765176). Widely expressed (PubMed:8953250). Expressed in the aerial tissues (e.g. cotyledons and leaf primordia), but not detected in the roots (PubMed:11743105). Expression levels display circadian oscillations under constant conditions, with a high amplitude and an early phase, with maximal expression around 4-6 hours of the light phase. Induced by light (PubMed:11743105). Transcripts levels oscillate weakly and proportionally to temperature, but protein levels are stable, with higher levels at low temperature (12 degrees Celsius) (PubMed:23511208). Accumulates in response to low blue light (LBL) (PubMed:26724867). The N-terminal domain CNT1 (1-489) is sufficient for autophosphorylation and is required for dimerization. The C-terminal domain CCT1 (490-681) of the homodimer binds to COP1. Autophosphorylated; in response to blue light and when in complex with FAD cofactor (PubMed:12846824, PubMed:14523249, PubMed:9651577, PubMed:17073458). Kinase activity is optimal in the presence of magnesium ions, about 30 percent of the optimal activity in the presence of manganese ions, but inactive with calcium ions (PubMed:17073458). Adopts an open conformation when phosphorylated upon photoexcitation and thus interacts with signaling partner proteins (PubMed:21841916). Prevents the shortening of period at 27 degrees Celsius, resulting in a long period phenotype. The double mutant cry1 cry2 is impaired in blue light signaling, resulting in long-period, lower-amplitude oscillations at 12 and 17 degrees Celsius and completely abolishing rhythms at 27 degrees Celsius (PubMed:23511208). Plants show reduced root and hypocotyl elongation in an anion channels activation-dependent manner at the plasma membrane, as well a reduced anthocyanin accumulation in blue light (PubMed:8528277, PubMed:12324610, PubMed:16703358, PubMed:21511871, PubMed:21511872, PubMed:9765547). Impaired blue/UV-A wavelengths-mediated inhibition of shoot regeneration (PubMed:22681544). Impaired detection of blue/green ratio in light leading to abnormal inhibition of hypocotyl growth (PubMed:20668058). Reduced attenuating effect of high fluence rates of blue light. This phenotype is stronger in the cry1 cry2 double mutant. Slow rate of curvature at low fluence rates of blue light in cry1 cry2 (PubMed:12857830). Lower anthocyanin accumulation in the phyB cry1 double mutant exposed to far-red light. Reduced chlorophyll levels in the phyB cry1 double mutant exposed to red light. In blue light, impaired cotyledon unfolding and smaller cotyledons, longer hypocotyls and less chlorophyll (PubMed:9733523). Impaired accumulation of reactive oxygen species (ROS) in double mutant cry1 cry2 exposed to high-intensity blue light (PubMed:25728686). Altered blue-light-triggered and singlet oxygen-mediated programmed cell death (PCD) (PubMed:17075038). The double mutant cry1 cry2 exhibits a reduced impact of near-null magnetic field on flowering in lower blue light intensity and short days (PubMed:26095447). Reduced hyponastic growth (differential growth-driven upward leaf movement) in low blue light fluence (PubMed:19558423). The double mutant cry1 cry2 is hyposensitive to the strigolactone analog GR24 (PubMed:24126495). The mutant cry1 exposed to a background of red light show severely impaired stomatal opening responses to blue light. The double mutant cry1 cry2 has reduced stomatal conductance, transpiration, and photosynthesis, particularly under the high irradiance of full sunlight at midday, associated with elevated abscisic acid levels (PubMed:22147516). The cry1 mutants grown in complete darkness have premature opening of the hypocotyl hook (PubMed:22855128). Reduced expression of nuclear genes encoding photoprotective components in response to extreme high light (PubMed:22786870). Reduced shade avoidance syndrome (SAS) when exposed to blue light attenuation (PubMed:21457375). Reduced growth at warm ambient temperatures (PubMed:21265897). Down-regulated local resistance and systemic acquired resistance (SAR) to Pseudomonas syringae pv. tomato (Pst.) DC3000 under continuous light conditions, leading to pathogen proliferation (PubMed:20053798). When grown in blue light, increased growth of lateral roots and reduced sensitivity to auxin (IAA) on this phenotype (PubMed:20133010). Belongs to the DNA photolyase class-1 family. Was originally thought to be a DNA photolyase.