Cited by 18

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Improved mammalian retromer cryo-EM structures reveal a new assembly interface

Kendall, Amy K., Chandra, Mintu, Xie, Boyang, Wan, William, Jackson, Lauren P.·2022·Journal of Biological Chemistry

Published version of a preprint

Overview

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.jbc.2022.102523

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

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.

A few free checks a day · papers already verified open instantly · results are public

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?

  • This interaction is unique to Retriever, as Retromer uses distinct surfaces to interact with adaptors, such as SNX3 and SNX27, or directly with cargoes, such as DMT1.

    “This interaction is unique to Retriever, as Retromer uses distinct surfaces to interact with adaptors, such as SNX3 and SNX27, or directly with cargoes, such as DMT126,29,34”

    From Structural basis for Retriever-SNX17 assembly and endosomal sorting (2024) · cites this paper as [34]

    The paper’s introductory text (labeled Abstract in our copy; no page number available) says retromer binds SNX3 and SNX27 and has been implicated in direct cargo recognition. It does not identify DMT1 as a directly bound cargo or establish that retromer uses distinct surfaces for those interactions. Nor does it establish that the interaction described by the citing paper is unique to Retriever. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • The precise mechanisms of cargo selection by Retriever have remained elusive.

    “Unlike the well-studied Retromer25,26,34, the precise mechanisms of cargo selection by Retriever have remained elusive37.”

    From Structural basis for Retriever-SNX17 assembly and endosomal sorting (2024) · cites this paper as [34]

    The paper’s introductory discussion (page unavailable) mentions Retriever only to identify VPS26C as a subunit of that complex. A search for Retriever and cargo-selection mechanisms found no passage in our copy saying whether those mechanisms remain elusive; the paper’s cargo-recognition discussion concerns Retromer instead. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 67

  1. Seaman, 1998, A membrane coat complex essential for endosome-to-Golgi retrograde transport in yeast, J. Cell Biol., 142, 665, 10.1083/jcb.142.3.665 · DOI · Paper page
  2. Seaman, 2004, Cargo-selective endosomal sorting for retrieval to the Golgi requires retromer, J. Cell, 165, 111, 10.1083/jcb.200312034 · DOI · Paper page
  3. Arighi, 2004, Role of the mammalian retromer in sorting of the cation-independent mannose 6-phosphate receptor, J. Cell Biol., 165, 123, 10.1083/jcb.200312055 · DOI · Paper page
  4. Lauffer, 2010, SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane, J. Cell Biol., 190, 565, 10.1083/jcb.201004060 · DOI · Paper page
  5. Temkin, 2011, SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors, Nat. Cell Biol., 13, 715, 10.1038/ncb2252 · DOI · Paper page
  6. Steinberg, 2013, A global analysis of SNX27-retromer assembly and cargo specificity reveals a function in glucose and metal ion transport, Nat. Cell Biol., 15, 461, 10.1038/ncb2721 · DOI · Paper page
  7. Choy, 2014, Retromer mediates a discrete route of local membrane delivery to dendrites, Neuron, 82, 55, 10.1016/j.neuron.2014.02.018 · DOI · Paper page
  8. Simonetti, 2018, Endosomal sorting: architecture of the retromer coat, Curr. Biol., 28, R1350, 10.1016/j.cub.2018.10.040 · DOI
  9. Chandra, 2021, Toward understanding the molecular role of SNX27/retromer in human health and disease, Front. Cell Dev. Biol., 9, 642378, 10.3389/fcell.2021.642378 · DOI
  10. Lu, 2014, From endosomes to the trans-Golgi network, Semin. Cell Dev. Biol., 31, 30, 10.1016/j.semcdb.2014.04.024 · DOI
  11. Fjorback, 2012, Retromer binds the FANSHY sorting motif in SorLA to regulate amyloid precursor protein sorting and processing, J. Neurosci., 32, 1467, 10.1523/JNEUROSCI.2272-11.2012 · DOI · Paper page
  12. Andersen, 2005, Neuronal sorting protein-related receptor sorLA/LR11 regulates processing of the amyloid precursor protein, Proc. Natl. Acad. Sci. U. S. A., 102, 13461, 10.1073/pnas.0503689102 · DOI · Paper page
  13. Yin, 2016, Vps35-dependent recycling of Trem2 regulates microglial function, Traffic, 17, 1286, 10.1111/tra.12451 · DOI · Paper page
  14. Reitz, 2011, SORCS1 alters amyloid precursor protein processing and variants may increase Alzheimer’s disease risk, Ann. Neurol., 69, 47, 10.1002/ana.22308 · DOI
  15. Mecozzi, 2014, Pharmacological chaperones stabilize retromer to limit APP processing, Nat. Chem. Biol., 10, 443, 10.1038/nchembio.1508 · DOI · Paper page
  16. Small, 2005, Model-guided microarray implicates the retromer complex in Alzheimer’s disease, Ann. Neurol., 58, 909, 10.1002/ana.20667 · DOI · Paper page
  17. Zimprich, 2011, A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease, Am. J. Hum. Genet., 89, 168, 10.1016/j.ajhg.2011.06.008 · DOI · Paper page
  18. Curtis, 2020, Dysregulation of the retromer complex system in Down syndrome, Ann. Neurol., 88, 137, 10.1002/ana.25752 · DOI · Paper page
  19. Filippone, 2021, Endosome dysregulation in Down syndrome: a potential contributor to Alzheimer disease pathology, Ann. Neurol., 90, 4, 10.1002/ana.26042 · DOI
  20. Romano-Moreno, 2017, Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL, Proc. Natl. Acad. Sci. U. S. A., 114, E11151, 10.1073/pnas.1715361115 · DOI
  21. Daniloski, 2021, Identification of required host factors for SARS-CoV-2 infection in human cells, Cell, 184, 92, 10.1016/j.cell.2020.10.030 · DOI
  22. Sztul, 2019, ARF GTPases and their GEFs and GAPs: concepts and challenges, Mol. Biol. Cell, 30, 1249, 10.1091/mbc.E18-12-0820 · DOI
  23. Chandra, 2020, Unveiling the cryo-EM structure of retromer, Biochem. Soc. Trans., 48, 2261, 10.1042/BST20200552 · DOI
  24. Nothwehr, 2000, Sorting of yeast membrane proteins into an endosome-to-Golgi pathway involves direct interaction of their cytosolic domains with Vps35p, J. Cell Biol., 151, 297, 10.1083/jcb.151.2.297 · DOI
  25. Kvainickas, 2017, Cargo-selective SNX-BAR proteins mediate retromer trimer independent retrograde transport, J. Cell Biol., 216, 3677, 10.1083/jcb.201702137 · DOI · Paper page
  26. Simonetti, 2019, Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins, Nat. Cell Biol., 21, 1219, 10.1038/s41556-019-0393-3 · DOI · Paper page
  27. Harrison, 2014, A mechanism for retromer endosomal coat complex assembly with cargo, Proc. Natl. Acad. Sci. U. S. A., 111, 267, 10.1073/pnas.1316482111 · DOI
  28. Bean, 2017, Cargo selectivity of yeast sorting nexins, Traffic, 18, 110, 10.1111/tra.12459 · DOI
  29. Lucas, 2016, Structural mechanism for cargo recognition by the retromer complex, Cell, 167, 1623, 10.1016/j.cell.2016.10.056 · DOI · Paper page
  30. Kovtun, 2018, Structure of the membrane-assembled retromer coat determined by cryo-electron tomography, Nature, 561, 561, 10.1038/s41586-018-0526-z · DOI · Paper page
  31. Leneva, 2021, Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly, Sci. Adv., 7, 10.1126/sciadv.abf8598 · DOI · Paper page
  32. Carlton, 2004, Sorting nexin-1 mediates tubular endosome-to-TGN transport through coincidence sensing of high- curvature membranes and 3-phosphoinositides, Curr. Biol., 14, 1791, 10.1016/j.cub.2004.09.077 · DOI · Paper page
  33. Simonetti, 2017, Sequence-dependent cargo recognition by SNX-BARs mediates retromer-independent transport of CI-MPR, J. Cell Biol., 216, 3695, 10.1083/jcb.201703015 · DOI · Paper page
  34. Strochlic, 2007, Grd19/Snx3p functions as a cargo-specific adapter for retromer-dependent endocytic recycling, J. Cell Biol., 177, 115, 10.1083/jcb.200609161 · DOI · Paper page
  35. Hierro, 2007, Functional architecture of the retromer cargo-recognition complex, Nature, 449, 1063, 10.1038/nature06216 · DOI · Paper page
  36. Collins, 2005, Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly, Nat. Struct. Mol. Biol., 12, 594, 10.1038/nsmb954 · DOI
  37. Collins, 2008, Structure of Vps26B and mapping of its interaction with the retromer protein complex, Traffic, 9, 366, 10.1111/j.1600-0854.2007.00688.x · DOI
  38. Kendall, 2020, Mammalian retromer is an adaptable scaffold for cargo sorting from endosomes, Structure, 28, 393, 10.1016/j.str.2020.01.009 · DOI
  39. Shi, 2006, The retromer subunit Vps26 has an arrestin fold and binds Vps35 through its C-terminal domain, Nat. Struct. Mol. Biol., 13, 540, 10.1038/nsmb1103 · DOI
  40. Wang, 2005, Crystal structure of human vacuolar protein sorting protein 29 reveals a phosphodiesterase/nuclease-like fold and two protein-protein interaction sites, J. Biol. Chem., 280, 22962, 10.1074/jbc.M500464200 · DOI
  41. Adams, 2010, PHENIX: a comprehensive, Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 · DOI · Paper page
  42. Chen, 2021, De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex, Sci. Adv., 7, 10.1126/sciadv.abg4007 · DOI · Paper page
  43. Norwood, 2010, Assembly and solution structure of the core retromer protein complex, Traffic, 12, 56, 10.1111/j.1600-0854.2010.01124.x · DOI · Paper page
  44. Greber, 2021, 2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942, Biophys. J., 120, 677, 10.1016/j.bpj.2020.12.030 · DOI
  45. Wan, 2017, Structure and assembly of the Ebola virus nucleocapsid, Nature, 551, 394, 10.1038/nature24490 · DOI
  46. Krissinel, 2007, Inference of macromolecular assemblies from crystalline state, J. Mol. Biol., 372, 774, 10.1016/j.jmb.2007.05.022 · DOI
  47. Braschi, 2010, Vps35 mediates vesicle transport between the mitochondria and peroxisomes, Curr. Biol., 20, 1310, 10.1016/j.cub.2010.05.066 · DOI
  48. Farmer, 2019, Retromer facilitates the localization of Bcl-xL to the mitochondrial outer membrane, Mol. Biol. Cell, 30, 1138, 10.1091/mbc.E19-01-0044 · DOI
  49. Kvainickas, 2019, Retromer and TBC1D5 maintain late endosomal RAB7 domains to enable amino acid-induced mTORC1 signaling, J. Cell Biol., 218, 3019, 10.1083/jcb.201812110 · DOI · Paper page
  50. Hesketh, 2020, The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids, Science, 370, 351, 10.1126/science.aaz0863 · DOI
  51. Roy, 2017, Autophagy-dependent shuttling of TBC1D5 controls plasma membrane translocation of GLUT1 and glucose uptake, Mol. Cell, 67, 84, 10.1016/j.molcel.2017.05.020 · DOI
  52. Farmer, 2018, Tying trafficking to fusion and fission at the mighty mitochondria, Traffic, 19, 569, 10.1111/tra.12573 · DOI
  53. Courtellemont, 2022, CROP: a retromer-PROPPIN complex mediating membrane fission in the endo-lysosomal system, EMBO J, 41, e109646, 10.15252/embj.2021109646 · DOI
  54. Morris, 2019, Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly, Nat. Struct. Mol. Biol., 26, 890, 10.1038/s41594-019-0292-0 · DOI
  55. Paraan, 2020, The structures of natively assembled clathrin-coated vesicles, Sci. Adv., 6, 10.1126/sciadv.aba8397 · DOI
  56. Wang, 1999, Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange site-directed mutagenesis, Biotechniques, 26, 680, 10.2144/99264st03 · DOI
  57. Scheres, 2012, Relion: implementation of a bayesian approach to cryo-EM structure determination, J. Struct. Biol., 180, 519, 10.1016/j.jsb.2012.09.006 · DOI · Paper page
  58. Zivanov, 2018, New tools for automated high-resolution cryo-EM structure determination in RELION-3, Elife, 7, 10.7554/eLife.42166 · DOI
  59. Carragher, 2000, Leginon: an automated system for acquisition of images from vitreous ice specimens, J. Struct. Biol., 132, 33, 10.1006/jsbi.2000.4314 · DOI
  60. Zheng, 2017, MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy, Nat. Methods, 14, 331, 10.1038/nmeth.4193 · DOI
  61. Zhang, 2016, Gctf: real-time CTF determination and correction, J. Struct. Biol., 193, 1, 10.1016/j.jsb.2015.11.003 · DOI
  62. Pettersen, 2004, UCSF Chimera--a visualization system for exploratory research and analysis, J. Comp. Chem., 25, 1605, 10.1002/jcc.20084 · DOI
  63. Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr, 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  64. Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073 · DOI · Paper page
  65. Williams, 2018, MolProbity: more and better reference data for improved all-atom structure validation, Protein Sci., 27, 293, 10.1002/pro.3330 · DOI · Paper page
  66. McNicholas, 2011, Presenting your structures: the CCP4mg molecular-graphics software, Acta Crystallogr. D Biol. Crystallogr., 67, 386, 10.1107/S0907444911007281 · DOI
  67. Ashkenazy, 2016, ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules, Nucl Acids Res, 10.1093/nar/gkw408 · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Kendall, A. K., Chandra, M., Xie, B., Wan, W., & Jackson, L. P.
Venue
Journal of Biological Chemistry
Publisher
Elsevier BV
Published
2022-11
Volume
298
Issue
11
Pages
102523
ISSN
0021-9258
Cited by
18
References
2
Language
en
Funders
  • NIH (U24 GM129539, R35GM119525, DP2GM146321)
  • Vanderbilt University
  • Simons Foundation (SF349247, R35GM119525, DP2GM146321)

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