CoChat
Sign Up
Cited by 63

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Structural basis for amyloidogenic peptide recognition by sorLA

Kitago, Yu, Nagae, Masamichi, Nakata, Zenzaburo, Yagi-Utsumi, Maho, Takagi-Niidome, Shizuka, Mihara, Emiko, Nogi, Terukazu, Kato, Koichi, Takagi, Junichi·2015·Nature Structural & Molecular Biology
DOI 10.1038/nsmb.2954
Open this paper in CoChat — free account

Abstract

SorLA is a neuronal sorting receptor considered to be a major risk factor for Alzheimer's disease. We have recently reported that it directs lysosomal targeting of nascent neurotoxic amyloid-β (Aβ) peptides by directly binding Aβ. Here, we determined the crystal structure of the human sorLA domain responsible for Aβ capture, Vps10p, in an unbound state and in complex with two ligands. Vps10p assumes a ten-bladed β-propeller fold with a large tunnel at the center. An internal ligand derived from the sorLA propeptide bound inside the tunnel to extend the β-sheet of one of the propeller blades. The structure of the sorLA Vps10p-Aβ complex revealed that the same site is used. Peptides are recognized by sorLA Vps10p in redundant modes without strict dependence on a particular amino acid sequence, thus suggesting a broad specificity toward peptides with a propensity for β-sheet formation.

Overview

Integrity signals

Registry

Crossref · 10.1038/nsmb.2954

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

  • Analysis of the impact of missense variants on SorLA structural stability suggested that the mutations had no major impact on SorLA global structure.

    “The analysis of the impact of missense variants on SorLA structural stability, focusing in the Vps10p domain of SorLA whose crystal structure was available [38], suggested that the mutations had no major impact on SorLA global structure.”

    From Impaired SorLA maturation and trafficking as a new mechanism for SORL1 missense variants in Alzheimer disease (2021) · cites this paper as [38]

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 47

  1. Jacobsen, L. et al. Molecular characterization of a novel human hybrid-type receptor that binds the α2-macroglobulin receptor-associated protein. J. Biol. Chem. 271, 31379–31383 (1996). · DOI · Paper page
  2. Yamazaki, H. et al. Elements of neural adhesion molecules and a yeast vacuolar protein sorting receptor are present in a novel mammalian low density lipoprotein receptor family member. J. Biol. Chem. 271, 24761–24768 (1996). · DOI
  3. Taira, K. et al. LR11, a mosaic LDL receptor family member, mediates the uptake of ApoE-rich lipoproteins in vitro. Arterioscler. Thromb. Vasc. Biol. 21, 1501–1506 (2001). · DOI
  4. Hampe, W. et al. A head-activator binding protein is present in hydra in a soluble and a membrane-anchored form. Development 126, 4077–4086 (1999). · DOI
  5. Schaller, H.C., Hermans-Borgmeyer, I. & Hoffmeister, S.A. Neuronal control of development in hydra. Int. J. Dev. Biol. 40, 339–344 (1996). · DOI
  6. Rezgaoui, M. et al. The neuropeptide head activator is a high-affinity ligand for the orphan G-protein-coupled receptor GPR37. J. Cell Sci. 119, 542–549 (2006). · DOI
  7. Scherzer, C.R. et al. Loss of apolipoprotein E receptor LR11 in Alzheimer disease. Arch. Neurol. 61, 1200–1205 (2004). · DOI · Paper page
  8. Andersen, O.M. et al. Neuronal sorting protein-related receptor sorLA/LR11 regulates processing of the amyloid precursor protein. Proc. Natl. Acad. Sci. USA 102, 13461–13466 (2005). · DOI · Paper page
  9. Rogaeva, E. et al. The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat. Genet. 39, 168–177 (2007). · DOI · Paper page
  10. Bettens, K. et al. SORL1 is genetically associated with increased risk for late-onset Alzheimer disease in the Belgian population. Hum. Mutat. 29, 769–770 (2008). · DOI
  11. Pottier, C. et al. High frequency of potentially pathogenic SORL1 mutations in autosomal dominant early-onset Alzheimer disease. Mol. Psychiatry 17, 875–879 (2012). · DOI · Paper page
  12. Caglayan, S. et al. Lysosomal sorting of amyloid-β by the SORLA receptor is impaired by a familial Alzheimer's disease mutation. Sci. Transl. Med. 6, 223ra20 (2014). · DOI · Paper page
  13. Marcusson, E.G., Horazdovsky, B.F., Cereghino, J.L., Gharakhanian, E. & Emr, S.D. The sorting receptor for yeast vacuolar carboxypeptidase Y is encoded by the VPS10 gene. Cell 77, 579–586 (1994). · DOI · Paper page
  14. Willnow, T.E., Petersen, C.M. & Nykjaer, A. VPS10P-domain receptors: regulators of neuronal viability and function. Nat. Rev. Neurosci. 9, 899–909 (2008). · DOI
  15. Quistgaard, E.M. et al. Ligands bind to Sortilin in the tunnel of a ten-bladed β-propeller domain. Nat. Struct. Mol. Biol. 16, 96–98 (2009). · DOI
  16. Jacobsen, L. et al. Activation and functional characterization of the mosaic receptor SorLA/LR11. J. Biol. Chem. 276, 22788–22796 (2001). · DOI · Paper page
  17. Rossi, A.M. & Taylor, C.W. Analysis of protein-ligand interactions by fluorescence polarization. Nat. Protoc. 6, 365–387 (2011). · DOI
  18. Deane, R. et al. LRP/amyloid beta-peptide interaction mediates differential brain efflux of Abeta isoforms. Neuron 43, 333–344 (2004). · DOI · Paper page
  19. Nakata, Z. et al. Crystallization and preliminary crystallographic analysis of human LR11 Vps10p domain. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67, 129–132 (2011). · DOI
  20. Chiti, F. & Dobson, C.M. Amyloid formation by globular proteins under native conditions. Nat. Chem. Biol. 5, 15–22 (2009). · DOI
  21. Trovato, A., Seno, F. & Tosatto, S.C.E. The PASTA server for protein aggregation prediction. Protein Eng. Des. Sel. 20, 521–523 (2007). · DOI
  22. Tycko, R. & Wickner, R.B. Molecular structures of amyloid and prion fibrils: consensus versus controversy. Acc. Chem. Res. 46, 1487–1496 (2013). · DOI
  23. Yagi-Utsumi, M. et al. NMR characterization of the interaction of GroEL with amyloid beta as a model ligand. FEBS Lett. 587, 1605–1609 (2013). · DOI
  24. Mittag, T. et al. Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. Proc. Natl. Acad. Sci. USA 105, 17772–17777 (2008). · DOI
  25. Libich, D.S., Fawzi, N.L., Ying, J.F. & Clore, G.M. Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR. Proc. Natl. Acad. Sci. USA 110, 11361–11366 (2013). · DOI
  26. Beglova, N. & Blacklow, S.C. The LDL receptor: how acid pulls the trigger. Trends Biochem. Sci. 30, 309–317 (2005). · DOI · Paper page
  27. Ohwaki, K. et al. A secreted soluble form of LR11, specifically expressed in intimal smooth muscle cells, accelerates formation of lipid-laden macrophages. Arterioscler. Thromb. Vasc. Biol. 27, 1050–1056 (2007). · DOI
  28. Mizushima, S. & Nagata, S. Pef-Bos, a powerful mammalian expression vector. Nucleic Acids Res. 18, 5322 (1990). · DOI
  29. Stanley, P. Chinese hamster ovary cell mutants with multiple glycosylation defects for production of glycoproteins with minimal carbohydrate heterogeneity. Mol. Cell. Biol. 9, 377–383 (1989). · DOI
  30. Fujii, Y. et al. PA tag: a versatile protein tagging system using a super high affinity antibody against a dodecapeptide derived from human podoplanin. Protein Expr. Purif. 95, 240–247 (2014). · DOI
  31. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997). · DOI · Paper page
  32. Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (2010). · DOI
  33. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). · DOI · Paper page
  34. Murshudov, G.N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011). · DOI
  35. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007). · DOI · Paper page
  36. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). · DOI · Paper page
  37. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010). · DOI · Paper page
  38. Yagi-Utsumi, M., Matsuo, K., Yanagisawa, K., Gekko, K. & Kato, K. Spectroscopic characterization of intermolecular interaction of amyloid β promoted on GM1 micelles. Int. J. Alzheimers Dis. 2011, 925073 (2010). · DOI
  39. Flanagan, J.G. et al. Alkaline phosphatase fusions of ligands or receptors as in situ probes for staining of cells, tissues, and embryos. Methods Enzymol. 327, 19–35 (2000). · DOI
  40. Tabata, S. et al. A rapid screening method for cell lines producing singly-tagged recombinant proteins using the “TARGET tag” system. J. Proteomics 73, 1777–1785 (2010). · DOI
  41. Pronk, S. et al. Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013). · DOI
  42. Oostenbrink, C., Villa, A., Mark, A.E. & Van Gunsteren, W.F. A biomolecular force field based on the free enthalpy of hydration and solvation: The gromos force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25, 1656–1676 (2004). · DOI
  43. Berendsen, H.J.C., Postma, J.P.M., Vangunsteren, W.F., Dinola, A. & Haak, J.R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690 (1984). · DOI
  44. Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447 (2008). · DOI
  45. Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N•log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993). · DOI
  46. Parrinello, M. & Rahman, A. Polymorphic transitions in single-crystals: a new molecular-dynamics method. J. Appl. Phys. 52, 7182–7190 (1981). · DOI
  47. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996). · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Kitago, Y., Nagae, M., Nakata, Z., Yagi-Utsumi, M., Takagi-Niidome, S., Mihara, E., Nogi, T., Kato, K., & Takagi, J.
Venue
Nature Structural & Molecular Biology
Publisher
Springer Science and Business Media LLC
Published
2015-02-02
Volume
22
Issue
3
Pages
199-206
ISSN
  • 1545-9993
  • 1545-9985
DOI
10.1038/nsmb.2954
Cited by
63
References
1
Language
en
Licence
www.springer.com/tdm (tdm)

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