CoChat
Sign Up
PreprintCited by 86Cellular transport and secretionEndoplasmic Reticulum Stress and DiseaseRNA and protein synthesis mechanisms

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

Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients

Open access
Miller-Vedam, Lakshmi E., Bräuning, Bastian, Popova, Katerina D., Oakdale, Nicole T. Schirle, Bonnar, Jessica L., Prabu, Jesuraj Rajan, Boydston, Elizabeth A., Sevillano, Natalia, Shurtleff, Matthew J., Stroud, Robert M., Craik, Charles S., Schulman, Brenda A., Frost, Adam, Weissman, Jonathan S.·2020·eLife
DOI 10.1101/2020.09.02.280008PMC PMC7785296

Preprint — published as 10.7554/elife.62611 · Paper page

Open this paper in CoChat — free account

Abstract

Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies revealed at least two separable EMC activities, as an insertase regulating tail-anchored protein levels and as a polytopic membrane protein holdase chaperone. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a novel, non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC’s multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.

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 · 10.1101/2020.09.02.280008

Cites

1 of 1 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

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: 123

  1. 2012, Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes, Genome Res, 23, 236
  2. 10.1016/j.ymeth.2011.07.005 · DOI
  3. 10.1107/s2059798318006551 · DOI
  4. 10.1093/nar/gky1151 · DOI
  5. 2017, Identification of Oxa1 Homologs Operating in the Eukaryotic Endoplasmic Reticulum, Cell Reports, 21, 3708, 10.1016/j.celrep.2017.12.006 · DOI · Paper page
  6. 2015, Specific Binding of Tetratricopeptide Repeat Proteins to Heat Shock Protein 70 (Hsp70) and Heat Shock Protein 90 (Hsp90) Is Regulated by Affinity and Phosphorylation, Biochemistry-us, 54, 7120, 10.1021/acs.biochem.5b00801 · DOI · Paper page
  7. Bai, L. , You, Q. , Feng, X. , Kovach, A. , Li, H ., 2020. Structure of the ER membrane complex, a transmembrane-domain insertase. Nature 1–4. https://doi.org/10.1038/s41586-020-2389-3 · DOI
  8. 10.7554/eLife.21470 · DOI
  9. 10.1039/c1mb05175j · DOI
  10. 10.1016/j.jsb.2017.03.007 · DOI
  11. 10.1002/(SICI)1521-1878(199911)21:11<932::AID-BIES5>3.0.CO;2-N · DOI
  12. 10.1016/j.str.2015.06.025 · DOI · Paper page
  13. 10.1038/nprot.2011.453 · DOI
  14. 10.1016/j.cell/2018.10.009 · DOI
  15. 2019, Intrinsic Structural Features of the Human IRE1α Transmembrane Domain Sense Membrane Lipid Saturation, Cell Reports, 27, 307, 10.1016/j.celrep.2019.03.017 · DOI
  16. 10.1038/ncb2383 · DOI
  17. 10.1038/s41467-019-08632-0 · DOI
  18. Cornell, C.E. , Mileant, A. , Thakkar, N. , Lee, K.K. , Keller, S.L. , 2020. Direct imaging of liquid domains in membranes by cryo-electron tomography. Proc National Acad Sci 202002245. https://doi.org/10.1073/pnas.2002245117 · DOI
  19. 2019, Emerging Diversity in Lipid–Protein Interactions, Chem Rev, 119, 5775, 10.1021/acs.chemrev.8b00451 · DOI
  20. 2018, Defining the physiological role of SRP in protein-targeting efficiency and specificity, Sci New York N Y, 359, 689, 10.1126/science.aar3607 · DOI
  21. 2008, MaxQuant enables high peptide identification rates, individualized p, p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol, 26, 1367
  22. 2000, Application of multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins Struct Funct Bioinform, 40, 502, 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q · DOI
  23. 10.1016/j.str.2015.08.002 · DOI
  24. 10.1073/pnas.1615719114 · DOI
  25. 10.1038/nature19356 · DOI · Paper page
  26. 10.1111/tra.12392 · DOI
  27. 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr Sect D Biological Crystallogr, 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  28. 2010, Features and development of Coot, Acta Crystallogr Sect D Biological Crystallogr, 66, 486, 10.1107/S0907444910007493 · DOI · Paper page
  29. 10.1002/pro.3235 · DOI · Paper page
  30. 10.1038/nprot.2014.173 · DOI
  31. 2019, TPR-containing proteins control protein organization and homeostasis for the endoplasmic reticulum, Crit Rev Biochem Mol, 54, 103, 10.1080/10409238.2019.1590305 · DOI
  32. 2017, The ER membrane protein complex is a transmembrane domain insertase, Science, 359, 470
  33. 10.1038/nprot.2017.094 · DOI
  34. 10.1016/j.molcel.2017.06.012 · DOI
  35. 10.1016/j.ajhg.2016.01.011 · DOI
  36. Heberle, F.A. , Doktorova, M. , Scott, H.L. , Skinkle, A.D. , Waxham, M.N. , Levental, I. , 2020. Direct label-free imaging of nanodomains in biomimetic and biological membranes by cryogenic electron microscopy. Proc National Acad Sci 202002200. https://doi.org/10.1073/pnas.2002200117 · DOI
  37. 2019, ER membrane protein complex is required for the insertions of late-synthesized transmembrane helices of Rh1 in Drosophila photoreceptors, Mol Biol Cell, 30, 2890, 10.1091/mbc.E19-08-0434 · DOI
  38. 10.1083/jcb.201802027 · DOI
  39. 2018, A particle-filter framework for robust cryo-EM 3D reconstruction, Nat Methods, 15, 1083, 10.1038/s41592-018-0223-8 · DOI
  40. 10.15252/embr.201643426 · DOI
  41. 10.1006/jmbi.1999.3091 · DOI
  42. 1994, A Model Recognition Approach to the Prediction of All-Helical Membrane Protein Structure and Topology, Biochemistry-us, 33, 3038, 10.1021/bi00176a037 · DOI
  43. 2009, Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum, Sci New York N Y, 323, 1693, 10.1126/science.1167983 · DOI
  44. 2010, hHSS1: a novel secreted factor and suppressor of glioma growth located at chromosome 19q13.33, J Neuro-oncol, 102, 197
  45. 10.1038/nprot.2012.085 · DOI
  46. 10.1038/nprot.2015.053 · DOI · Paper page
  47. 10.1016/j.ymeth.2011.09.012 · DOI
  48. 10.7554/eLife.18722.001 · DOI
  49. 10.1006/jmbi.2000.4315 · DOI · Paper page
  50. 2017, Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp, Frontiers Mol Biosci, 4, 68, 10.3389/fmolb.2017.00068 · DOI
  51. 10.1007/s12192-018-0908-z · DOI
  52. 2014, Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase, Sci Rep-uk, 4, 7299, 10.1038/srep07299 · DOI
  53. 10.1371/journal.pbio.1001969 · DOI · Paper page
  54. 10.1038/s41586-018-0833-4 · DOI · Paper page
  55. 2019, The ER Membrane Protein Complex Promotes Biogenesis of Dengue and Zika Virus Non-structural Multi-pass Transmembrane Proteins to Support Infection, Cell Reports, 27, 1666, 10.1016/j.celrep.2019.04.051 · DOI
  56. 10.1186/gm404 · DOI
  57. 10.1038/nmeth.2472 · DOI
  58. 2019, Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix, Acta Crystallogr Sect D, 75, 861, 10.1107/S2059798319011471 · DOI · Paper page
  59. 2002, An ER Membrane Protein, Sop4, Facilitates ER Export of the Yeast Plasma Membrane [H+]ATPase, Pma1. Traffic, 3, 730, 10.1034/j.1600-0854.2002.31005.x · DOI
  60. 10.1126/science.252.5009.1162 · DOI · Paper page
  61. 10.1021/acs.chemrev.8b00532 · DOI
  62. 2020, Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects, J Clin Invest, 130, 813, 10.1172/JCI129308 · DOI
  63. 10.1016/j.jsb.2005.07.007 · DOI
  64. 10.1073/pnas.0307332101 · DOI
  65. 10.7554/eLife.01456 · DOI
  66. 2019, The ER membrane protein complex is required to ensure correct topology and stable expression of flavivirus polyproteins, Elife, 8, e48469, 10.7554/eLife.48469 · DOI
  67. 10.1006/jmbi.2000.4042 · DOI
  68. 2020, The architecture of EMC reveals a path for membrane protein insertion, Elife, 9, e57887, 10.7554/eLife.57887 · DOI
  69. 2005, Exploiting heterogeneous sequence properties improves prediction of protein disorder, Proteins Struct Funct Bioinform, 61, 176, 10.1002/prot.20735 · DOI
  70. 10.1110/ps.9.6.1162 · DOI
  71. 10.1186/1471-2105-7-208 · DOI
  72. 2020, TMEM16K is an interorganelle regulator of endosomal sorting, Nat Commun, 11, 3298, 10.1038/s41467-020-17016-8 · DOI
  73. 10.1002/jcc.20084 · DOI
  74. 10.1038/ncomms14516 · DOI
  75. Pleiner, T. , Tomaleri, G.P. , Januszyk, K. , Inglis, A.J. , Hazu, M. , Voorhees, R.M. , 2020. Structural basis for membrane insertion by the human ER membrane protein complex. Science eabb5008. https://doi.org/10.1126/science.abb5008 · DOI
  76. 10.1021/pr501039k · DOI
  77. 10.1038/nmeth.4169 · DOI · Paper page
  78. Punjani, A. , Zhang, H. , Fleet, D.J. , 2019. Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction. Biorxiv 2019.12.15.877092. https://doi.org/10.1101/2019.12.15.877092 · DOI
  79. Punjani, A. , Fleet, D.J. , 2020. 3D Variability Analysis: Directly resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM images. Biorxiv 2020.04.08.032466. https://doi.org/10.1101/2020.04.08.032466 · DOI
  80. 2009, Structure prediction for CASP8 with all-atom refinement using Rosetta, Proteins Struct Funct Bioinform, 77, 89, 10.1002/prot.22540 · DOI
  81. 10.1126/science.aaz3505 · DOI
  82. 2020, Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER, J Struct Biol, 211, 107545, 10.1016/j.jsb.2020.107545 · DOI
  83. 10.1038/nprot.2007.261 · DOI · Paper page
  84. 2015, SMP-domain proteins at membrane contact sites: Structure and function, Biochim Biophys Acta, 1861, 924
  85. 10.1073/pnas.1216154110 · DOI
  86. 10.1016/S0076-6879(09)64011-8 · DOI
  87. 10.1006/jsbi.2001.4336 · DOI
  88. 10.1016/S1046-2023(05)80070-2 · DOI
  89. 10.1038/nprot.2010.5 · DOI
  90. 2018, Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions, Biophys J, 114, 355, 10.1016/j.bpj.2017.11.021 · DOI
  91. 10.1038/35020586 · DOI · Paper page
  92. 10.7554/eLife.06306 · DOI
  93. 2016, Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics, Cell Reports, 16, 232, 10.1016/j.celrep.2016.06.028 · DOI
  94. 10.1016/S0092-8674(00)80830-2 · DOI · Paper page
  95. 10.1093/molbev/msm211 · DOI
  96. 2020, Lipid-Protein Interactions Are a Unique Property and Defining Feature of G Protein-Coupled Receptors, Biophys J, 118, 1887, 10.1016/j.bpj.2020.03.008 · DOI
  97. 10.1038/nprot.2008.156 · DOI
  98. 10.7554/eLife.37018 · DOI
  99. 10.1016/j.str.2013.08.005 · DOI
  100. 2014, ResLog plots as an empirical metric of the quality of cryo-EM reconstructions, J Struct Biol, 185, 418, 10.1016/j.jsb.2013.12.010 · DOI
  101. 10.1073/pnas.0907522106 · DOI
  102. 10.1074/jbc.RA119.008299 · DOI
  103. 10.1172/JCI94152 · DOI
  104. 2019, Proteomic Analysis Identifies Membrane Proteins Dependent on the ER Membrane Protein Complex, Cell Reports, 28, 2517, 10.1016/j.celrep.2019.08.006 · DOI
  105. 2018, The ER membrane protein complex promotes biogenesis of sterol-related enzymes maintaining cholesterol homeostasis, J Cell Sci, 132, jcs223453
  106. 10.1242/jcs.243519 · DOI
  107. 10.1073/pnas.1217611110 · DOI
  108. 2002, Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics, Biochemistry-us, 41, 13575, 10.1021/bi0261387 · DOI
  109. 10.1016/j.jmb.2004.02.002 · DOI
  110. Wainberg, M. , Kamber, R.A. , Balsubramani, A. , Meyers, R.M. , Sinnott-Armstrong, N. , Hornburg, D. , Jiang, L. , Chan, J. , Jian, R. , Gu, M. , Shcherbina, A. , Dubreuil, M.M. , Spees, K. , Snyder, M.P. , Kundaje, A. , Bassik, M.C. , 2019. A genome-wide almanac of co-essential modules assigns function to uncharacterized genes. Biorxiv 827071. https://doi.org/10.1101/827071 · DOI · Paper page
  111. 10.1093/bioinformatics/btp033 · DOI
  112. 10.1073/pnas.1604935113 · DOI
  113. Wideman, J.G ., 2015. The ubiquitous and ancient ER membrane protein complex (EMC): tether or not? F 1000research 4, 624. https://doi.org/10.12688/f1000research.6944.1 · DOI
  114. 10.1016/j.str.2012.02.017 · DOI
  115. 2020, ER complex proteins are required for rhodopsin biosynthesis and photoreceptor survival in Drosophila and mice, Cell Death Differ, 27, 646, 10.1038/s41418-019-0378-6 · DOI
  116. 10.1038/nmeth.3213 · DOI · Paper page
  117. 10.1016/j.jsb.2015.11.003 · DOI
  118. 10.1016/j.cell.2017.08.036 · DOI
  119. 10.1186/1471-2105-9-40 · DOI · Paper page
  120. 10.1038/nmeth.4193 · DOI
  121. 2018, EMC10 governs male fertility via maintaining sperm ion balance, J Mol Cell Biol, 10, 503, 10.1093/jmcb/mjy024 · DOI
  122. 10.1016/j.jmb.2017.12.00 · DOI
  123. 10.7554/eLife.42166 · DOI

Metadata

Authors
Miller-Vedam, L. E., Bräuning, B., Popova, K. D., Oakdale, N. T. S., Bonnar, J. L., Prabu, J. R., Boydston, E. A., Sevillano, N., Shurtleff, M. J., Stroud, R. M., Craik, C. S., Schulman, B. A., Frost, A., & Weissman, J. S.
Affiliations
  • University of California, San Francisco (US)
  • Max Planck Institute of Biochemistry (DE)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Schulman, Brenda A.
  • Frost, Adam
  • Weissman, Jonathan S.
ORCID
Venue
eLife
Publisher
openRxiv
Published
2020-09-02
Volume
9
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2020.09.02.280008
PMC
PMC7785296
OpenAlex
W3110296556
Cited by
86
References
1
Citations by year
2026: 8 · 2025: 10 · 2024: 13 · 2023: 21 · 2022: 15 · 2021: 17 · 2020: 2
FWCI
6.85
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
  • eScholarship (California Digital Library) (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Funders
  • Howard Hughes Medical Institute (55108523)
  • Jane Coffin Childs Memorial Fund for Medical Research
  • Helen Hay Whitney Foundation
  • Chan Zuckerberg Initiative
  • Deutsche Forschungsgemeinschaft (Leibniz Prize SCHU 3196/1-1)
  • Max-Planck-Gesellschaft
  • Peter und Traudl Engelhorn Stiftung
  • National Institutes of Health (1s10od021741-01, 1DP2OD017690-01, 1s10od020054-01, 1s10od021596-01, GM 24485)
  • University of California, San Francisco
  • National Cancer Institute (P41CA196276, P30CA082103)
  • National Institute of General Medical Sciences (T32GM008284, R37GM024485, P41GM103311, R01GM024485, R01GM129325)
  • National Institute of Allergy and Infectious Diseases (P50AI150476)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Endoplasmic Reticulum Stress and Disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
electromagnetic compatibility, membrane protein biogenesis, endoplasmic reticulum, tail-anchored proteins, polytopic membrane proteins, protein insertion
MeSH terms
Endoplasmic Reticulum, Humans, Intracellular Membranes, Membrane Proteins, Saccharomyces cerevisiae, Blotting, Western, Sequence Alignment, Protein Structure, Tertiary, Saccharomyces cerevisiae Proteins

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