SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket
Open accessAbstract
The cryptochrome (CRY) flavoproteins act as blue-light receptors in plants and insects, but perform light-independent functions at the core of the mammalian circadian clock. To drive clock oscillations, mammalian CRYs associate with the Period proteins (PERs) and together inhibit the transcription of their own genes. The SCF(FBXL3) ubiquitin ligase complex controls this negative feedback loop by promoting CRY ubiquitination and degradation. However, the molecular mechanisms of their interactions and the functional role of flavin adenine dinucleotide (FAD) binding in CRYs remain poorly understood. Here we report crystal structures of mammalian CRY2 in its apo, FAD-bound and FBXL3-SKP1-complexed forms. Distinct from other cryptochromes of known structures, mammalian CRY2 binds FAD dynamically with an open cofactor pocket. Notably, the F-box protein FBXL3 captures CRY2 by simultaneously occupying its FAD-binding pocket with a conserved carboxy-terminal tail and burying its PER-binding interface. This novel F-box-protein-substrate bipartite interaction is susceptible to disruption by both FAD and PERs, suggesting a new avenue for pharmacological targeting of the complex and a multifaceted regulatory mechanism of CRY ubiquitination.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The crystal structure of FBXL3 bound to a substrate does not reveal any well-defined pocket along the LRR domain.
“The crystal structure of FBXL3 bound to a substrate does not reveal any well-defined pocket along the LRR domain 115”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [115]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475 · see citing works
Colowick, S. P., Joshi, M. D., Jagannathan, & KAPLAN, N. O. (1966) · Cited by 26,137 · see citing works
The CCP4 suite: programs for protein crystallography
Number Collaborative Computational Project (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994003112 · Cited by 17,299 · see citing works
Coordination of circadian timing in mammals
Reppert, S. M., & Weaver, D. R. (2002) · Nature · doi:10.1038/nature00965 · Cited by 4,379 · see citing works
<i>PHENIX</i> : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361 · see citing works
Dibner, C., Schibler, U., & Albrecht, U. (2010) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021909-135821 · Cited by 2,421 · see citing works
Circadian integration of metabolism and energetics
Bass, J., & Takahashi, J. S. (2010) · Science · doi:10.1126/science.1195027 · Cited by 1,910 · see citing works
Mechanism of auxin perception by the TIR1 ubiquitin ligase
Tan, X., Calderon-Villalobos, L. I. A., Sharon, M., Zheng, C., Robinson, C. V., Estelle, M., & Zheng, N. (2007) · Nature · doi:10.1038/nature05731 · Cited by 1,688 · see citing works
Self-citationMammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms
Horst, G. T. J. V. D., Muijtjens, M., Kobayashi, K., Takano, R., Kanno, S.-I., Takao, M., Wit, J. D., Verkerk, A., Eker, A. P. M., Leenen, D. V., et al. (1999) · Nature · doi:10.1038/19323 · Cited by 1,402 · see citing works
Interacting molecular loops in the mammalian circadian clock
Shearman, L. P., Sriram, S., Weaver, D. R., Maywood, E. S., Chaves, I., Zheng, B., Kume, K., Lee, C. C., van der, G. T. J., Horst, et al. (2000) · Science · doi:10.1126/science.288.5468.1013 · Cited by 1,367 · see citing works
Posttranslational Mechanisms Regulate the Mammalian Circadian Clock
Lee, C., Etchegaray, J., Cagampang, F. R. A., Loudon, A. S. I., & Reppert, S. M. (2001) · Cell · doi:10.1016/s0092-8674(01)00610-9 · Cited by 1,158 · see citing works
The cryb mutation identifies cryptochrome as a circadian photoreceptor in Drosophila
Stanewsky, R., Kaneko, M., Emery, P., Beretta, B., Wager-Smith, K., Kay, S. A., Rosbash, M., & Hall, J. C. (1998) · Cell · doi:10.1016/s0092-8674(00)81638-4 · Cited by 968 · see citing works
AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation
Lamia, K. A., Sachdeva, U. M., DiTacchio, L., Williams, E. C., Alvarez, J. G., Egan, D. F., Vasquez, D. S., Juguilon, H., Panda, S., Shaw, R. J., et al. (2009) · Science · doi:10.1126/science.1172156 · Cited by 958 · see citing works
Green, C. B., Takahashi, J. S., & Bass, J. (2008) · Cell · doi:10.1016/j.cell.2008.08.022 · Cited by 902 · cited 4× · see citing works
“Two shorter versions of the protein, mCRY2 (1-527) and mCRY2 (1-512), were subsequently purified.”
InfluentialThe cryptochromes: blue light photoreceptors in plants and animals
Chaves, I., Pokorny, R., Byrdin, M., Hoang, N., Ritz, T., Brettel, K., Essen, L.-O., van der Horst, G. T. J., Batschauer, A., & Ahmad, M. (2011) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042110-103759 · Cited by 845 · see citing works
Light-Independent Role of CRY1 and CRY2 in the Mammalian Circadian Clock
Griffin, E. A., Staknis, D., & Weitz, C. J. (1999) · Science · doi:10.1126/science.286.5440.768 · Cited by 646 · see citing works
Crosstalk between components of circadian and metabolic cycles in mammals
Asher, G., & Schibler, U. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.01.006 · Cited by 601 · see citing works
Crystal Structure of DNA Photolyase from Escherichia coli
Park, H.-W., Kim, S., Sancar, A., & Deisenhofer, J. (1995) · Science · doi:10.1126/science.7604260 · Cited by 585 · see citing works
Siepka, S. M., Yoo, S. H., Park, J., Song, W., Kumar, V., Hu, Y., Lee, C., & Takahashi, J. S. (2007) · Cell · doi:10.1016/j.cell.2007.04.030 · Cited by 536 · see citing works
Direct Interaction of Arabidopsis Cryptochromes with COP1 in Light Control Development
Wang, H., Ma, L., Li, J.-M., Zhao, H., & Deng, X. W. (2001) · Science · doi:10.1126/science.1063630 · Cited by 525 · see citing works
Busino, L., Bassermann, F. C., Maiolica, A., Lee, C., Nolan, P. M., Godinho, S. I. H., Draetta, G. F., & Pagano, M. (2007) · Science · doi:10.1126/science.1141194 · Cited by 509 · see citing works
Self-citationIdentification of Small Molecule Activators of Cryptochrome
Hirota, T., Lee, J. W., John, P. C. S., Sawa, M., Iwaisako, K., Noguchi, T., Pongsawakul, P. Y., Sonntag, T., Welsh, D. K., Brenner, D. A., et al. (2012) · Science · doi:10.1126/science.1223710 · Cited by 500 · see citing works
Cryptochrome Structure and Signal Transduction
Lin, C., & Shalitin, D. (2003) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.54.110901.160901 · Cited by 485 · see citing works
The After-Hours Mutant Reveals a Role for Fbxl3 in Determining Mammalian Circadian Period
Godinho, S. I. H., Maywood, E. S., Shaw, L. E., Tucci, V., Barnard, A. R., Busino, L., Pagano, M., Kendall, R., Quwailid, M. M., Romero, M. R., et al. (2007) · Science · doi:10.1126/science.1141138 · Cited by 468 · see citing works
Self-citationYuan, Q., Metterville, D. R., Briscoe, A. D., & Reppert, S. M. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm011 · Cited by 402 · see citing works
The Signaling Mechanism of Arabidopsis CRY1 Involves Direct Interaction with COP1
Yang, H., Tang, R., & Cashmore, A. R. (2001) · The Plant Cell · doi:10.1105/tpc.010367 · Cited by 345 · see citing works
Structural Basis of the Cks1-Dependent Recognition of p27Kip1 by the SCFSkp2 Ubiquitin Ligase
Hao, B., Zheng, N., Schulman, B. A., Wu, G., Miller, J. J., Pagano, M., & Pavletich, N. P. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.09.003 · Cited by 306 · see citing works
Self-citationJETLAG Resets the Drosophila Circadian Clock by Promoting Light-Induced Degradation of TIMELESS
Koh, K., Zheng, X., & Sehgal, A. (2006) · Science · doi:10.1126/science.1124951 · Cited by 293 · see citing works
Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana
Brautigam, C. A., Smith, B. S., Ma, Z., Palnitkar, M., Tomchick, D. R., Machius, M., & Deisenhofer, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404851101 · Cited by 293 · see citing works
Yagita, K., Tamanini, F., Yasuda, M., Hoeijmakers, J. H. J., van der Horst, G. T. J., & Okamura, H. (2002) · The EMBO Journal · doi:10.1093/emboj/21.6.1301 · Cited by 271 · see citing works
Zhu, H., Yuan, Q., Froy, O., Casselman, A., & Reppert, S. M. (2005) · Current Biology · doi:10.1016/j.cub.2005.11.030 · Cited by 238 · see citing works
Chen, R., Schirmer, A. E., Lee, Y., Lee, H.-M., Kumar, V., Yoo, S. H., Takahashi, J. S., & Lee, C. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.10.012 · Cited by 225 · see citing works
Peschel, N., Chen, K., Szabo, G., & Stanewsky, R. (2009) · Current Biology · doi:10.1016/j.cub.2008.12.042 · Cited by 215 · see citing works
Crystal Structure and Mechanism of a DNA (6‐4) Photolyase
Maul, M. J., Barends, T. R. M., Glas, A. F., Cryle, M. J., Domratcheva, T. M., Schneider, S., Schlichting, I., & Carell, T. (2008) · Angewandte Chemie International Edition · doi:10.1002/anie.200804268 · Cited by 197 · see citing works
Searching for a photocycle of the cryptochrome photoreceptors
Liu, B., Liu, H., Zhong, D., & Lin, C. (2010) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2010.09.005 · Cited by 169 · see citing works
Structure of full-length Drosophila cryptochrome
Zoltowski, B. D., Vaidya, A. T., Top, D., Widom, J. M., Young, M. W., & Crane, B. R. (2011) · Nature · doi:10.1038/nature10618 · Cited by 162 · see citing works
Structural biology of DNA photolyases and cryptochromes
Müller, M., & Carell, T. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.05.003 · Cited by 125 · see citing works
Hitomi, K., DiTacchio, L., Arvai, A. S., Yamamoto, J., Kim, S., Todo, T., Tainer, J. A., Iwai, S., Panda, S., & Getzoff, E. D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809180106 · Cited by 123 · see citing works
Chaves, I., Yagita, K., Barnhoorn, S., et al. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.26.5.1743-1753.2006 · Cited by 104 · see citing works
Structure and Function of Animal CryptochromesPreprint
Öztürk, N., Song, S.-H., Özgür, S., Selby, C. P., Morrison, L., Partch, C. L., Zhong, D., & Sancar, A. (2007) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2007.72.015 · Cited by 103 · see citing works
Serine phosphorylation of mCRY1 and mCRY2 by mitogen‐activated protein kinase
Sanada, K., Harada, Y., Sakai, M., Todo, T., & Fukada, Y. (2004) · Genes to Cells · doi:10.1111/j.1356-9597.2004.00758.x · Cited by 69 · see citing works
Özber, N., Barış, İ., Tatlici, G., et al. (2010) · BMC Molecular Biology · doi:10.1186/1471-2199-11-69 · Cited by 35 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Ubiquitin ligases: structure, function, and regulation
Zheng, N., & Shabek, N. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060815-014922 · Cited by 1,499 · see citing works
Molecular architecture of the mammalian circadian clock
Partch, C. L., Green, C. B., & Takahashi, J. S. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.07.002 · Cited by 1,449 · see citing works
Targeted protein degradation: expanding the toolbox
Schapira, M., Calabrese, M. F., Bullock, A. N., & Crews, C. M. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-019-0047-y · Cited by 960 · see citing works
Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation
Scott, D. C., Rhee, D. Y., Duda, D. M., Kelsall, I. R., Olszewski, J. L., Paulo, J. A., de Jong, A., Ovaa, H., Alpi, A. F., Harper, J. W., et al. (2016) · Cell · doi:10.1016/j.cell.2016.07.027 · Cited by 229 · see citing works
Ubiquitin ligation to F-box protein targets by SCF–RBR E3–E3 super-assembly
Horn-Ghetko, D., Krist, D. T., Prabu, J. R., Baek, K., Mulder, M. P. C., Klügel, M., Scott, D. C., Ovaa, H., Kleiger, G., & Schulman, B. A. (2021) · Nature · doi:10.1038/s41586-021-03197-9 · Cited by 187 · see citing works
Photolyase: Dynamics and electron-transfer mechanisms of DNA repair
Zhang, M., Wang, L., & Zhong, D. (2017) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2017.08.007 · Cited by 115 · see citing works
Recognition of the Diglycine C-End Degron by CRL2KLHDC2 Ubiquitin Ligase
Rusnac, D.-V., Lin, H.-C., Canzani, D., Tien, K. X., Hinds, T. R., Tsue, A. F., Bush, M. F., Yen, H.-C. S., & Zheng, N. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.021 · Cited by 93 · see citing works
Self-citationKumanomidou, T., Nishio, K., Takagi, K., Nakagawa, T., Suzuki, A., Yamane, T., Tokunaga, F., Iwai, K., Murakami, A., Yoshida, Y., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0140366 · Cited by 21 · see citing works
Canzani, D., Rusnac, D.-V., Zheng, N., & Bush, M. F. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02331 · Cited by 11 · see citing works
Self-citation
- Authors
- Xing, W., Busino, L., Hinds, T. R., Marionni, S. T., Saifee, N. H., Bush, M. F., Pagano, M., & Zheng, N.
- Affiliations
- University of Washington (US)
- New York University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Zheng, Ning
- ORCID
- Venue
- Nature
- Published
- 2013-03-17
- Volume
- 496
- Issue
- 7443
- Pages
- 64-68
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3618506
- OpenAlex
- W2062830884
- Cited by
- 234
- References
- 42
- Citations by year
- 2026: 19 · 2025: 20 · 2024: 7 · 2023: 16 · 2022: 20 · 2021: 14 · 2020: 28 · 2019: 12 · 2018: 15 · 2017: 15 · 2016: 21 · 2015: 21 · 2014: 17 · 2013: 9
- FWCI
- 12.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Heart, Lung, and Blood Institute (T32HL007151)
- National Cancer Institute (R01CA107134, K99CA166181, R21CA161108, R37CA076584)
- National Institute of General Medical Sciences (R01GM057587)
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- CRY2, FBXL3, FAD binding, F-box protein, circadian clock, PERIOD protein, ubiquitination, protein degradation, crystal structure, blue-light photoreceptor
- MeSH terms
- Animals, Apoproteins, Binding Sites, Deoxyribodipyrimidine Photo-Lyase, Drosophila melanogaster, Flavin-Adenine Dinucleotide, Humans, Models, Molecular, Substrate Specificity, Protein Structure, Tertiary, Crystallography, X-Ray, F-Box Proteins, S-Phase Kinase-Associated Proteins, SKP Cullin F-Box Protein Ligases, Mice, Cryptochromes, Hydrophobic and Hydrophilic Interactions
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
