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Cited by 78Trace Elements in HealthAdvanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations

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Xue, Jing, Xie, Tian, Zeng, Weizhong, Jiang, Youxing, Bai, Xiao-chen·2020·eLife
DOI 10.7554/elife.58823PMC PMC7428307
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Abstract

ZnT8 is a Zn 2+ /H + antiporter that belongs to SLC30 family and plays an essential role in regulating Zn 2+ accumulation in the insulin secretory granules of pancreatic β cells. However, the Zn 2+ /H + exchange mechanism of ZnT8 remains unclear due to the lack of high-resolution structures. Here, we report the cryo-EM structures of human ZnT8 (HsZnT8) in both outward- and inward-facing conformations. HsZnT8 forms a dimeric structure with four Zn 2+ binding sites within each subunit: a highly conserved primary site in transmembrane domain (TMD) housing the Zn 2+ substrate; an interfacial site between TMD and C-terminal domain (CTD) that modulates the Zn 2+ transport activity of HsZnT8; and two adjacent sites buried in the cytosolic domain and chelated by conserved residues from CTD and the His-Cys-His (HCH) motif from the N-terminal segment of the neighboring subunit. A comparison of the outward- and inward-facing structures reveals that the TMD of each HsZnT8 subunit undergoes a large structural rearrangement, allowing for alternating access to the primary Zn 2+ site during the transport cycle. Collectively, our studies provide the structural insights into the Zn 2+ /H + exchange mechanism of HsZnT8.

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  • The N-terminus of the ZnT family modulates transporter activity by facilitating either protein interactions or zinc binding.

    “It has been suggested that the N-terminus of the ZnT family modulates the transporter activity by facilitating either protein interactions or zinc binding [42,43].”

    From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [43]

    The Results section (“Zn2+ binding sites in CTD”; page unavailable) shows that ZnT8’s N-terminal HCH motif binds zinc and that deleting it reduces zinc uptake. It says the motif is conserved in some ZnT subfamilies, but does not establish this mechanism across the family or say that the N-terminus modulates activity by facilitating protein interactions. (LLM, conf=0.86)

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Research works printed but not linked: 35

  1. Adams PD Afonine PV Bunkóczi G Chen VB Davis IW Echols N Headd JJ Hung LW Kapral GJ Grosse-Kunstleve RW McCoy AJ Moriarty NW Oeffner R Read RJ Richardson DC Richardson JS Terwilliger TC Zwart PH 2010 PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallographica Section D Biological Crystallography 66 213 221 10.1107/S0907444909052925 20124702 PMC2815670 · DOI · Paper page
  2. Arkhipova V Guskov A Slotboom DJ 2020 Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment Nature Communications 11 998 10.1038/s41467-020-14834-8 32081874 PMC7035293 · DOI
  3. Chabosseau P Rutter GA 2016 Zinc and diabetes Archives of Biochemistry and Biophysics 611 79 85 10.1016/j.abb.2016.05.022 27262257 · DOI
  4. Chen VB Arendall WB Headd JJ Keedy DA Immormino RM Kapral GJ Murray LW Richardson JS Richardson DC 2010 MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallographica Section D Biological Crystallography 66 12 21 10.1107/S0907444909042073 20057044 PMC2803126 · DOI · Paper page
  5. Chimienti F Devergnas S Favier A Seve M 2004 Identification and cloning of a beta-cell-specific zinc transporter, ZnT-8, localized into insulin secretory granules Diabetes 53 2330 2337 10.2337/diabetes.53.9.2330 15331542 · DOI
  6. Chovancova E Pavelka A Benes P Strnad O Brezovsky J Kozlikova B Gora A Sustr V Klvana M Medek P Biedermannova L Sochor J Damborsky J 2012 CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures PLOS Computational Biology 8 e1002708 10.1371/journal.pcbi.1002708 23093919 PMC3475669 · DOI
  7. Chowanadisai W Lönnerdal B Kelleher SL 2006 Identification of a mutation in SLC30A2 (ZnT-2) in women with low milk zinc concentration that results in transient neonatal zinc deficiency Journal of Biological Chemistry 281 39699 39707 10.1074/jbc.M605821200 17065149 · DOI
  8. Coudray N Valvo S Hu M Lasala R Kim C Vink M Zhou M Provasi D Filizola M Tao J Fang J Penczek PA Ubarretxena-Belandia I Stokes DL 2013 Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy PNAS 110 2140 2145 10.1073/pnas.1215455110 23341604 PMC3568326 · DOI
  9. Danev R Baumeister W 2016 Cryo-EM single particle analysis with the volta phase plate eLife 5 e13046 10.7554/eLife.13046 26949259 PMC4850076 · DOI
  10. Davidson HW Wenzlau JM O'Brien RM 2014 Zinc transporter 8 (ZnT8) and β cell function Trends in Endocrinology & Metabolism 25 415 424 10.1016/j.tem.2014.03.008 24751356 PMC4112161 · DOI
  11. Eide DJ 2006 Zinc transporters and the cellular trafficking of zinc Biochimica Et Biophysica Acta (BBA) - Molecular Cell Research 1763 711 722 10.1016/j.bbamcr.2006.03.005 16675045 · DOI · Paper page
  12. Emsley P Lohkamp B Scott WG Cowtan K 2010 Features and development of coot Acta Crystallographica. Section D, Biological Crystallography 66 486 501 10.1107/S0907444910007493 20383002 PMC2852313 · DOI
  13. Hessels AM Chabosseau P Bakker MH Engelen W Rutter GA Taylor KM Merkx M 2015 eZinCh-2: a versatile, genetically encoded FRET sensor for cytosolic and intraorganelle zn(2+) Imaging ACS Chemical Biology 10 2126 2134 10.1021/acschembio.5b00211 26151333 PMC4577962 · DOI
  14. Hirschi M Johnson ZL Lee SY 2017 Visualizing multistep elevator-like transitions of a nucleoside transporter Nature 545 66 70 10.1038/nature22057 28424521 PMC5567992 · DOI
  15. Hoch E Lin W Chai J Hershfinkel M Fu D Sekler I 2012 Histidine pairing at the metal transport site of mammalian ZnT transporters controls Zn2+ over Cd2+ selectivity PNAS 109 7202 7207 10.1073/pnas.1200362109 22529353 PMC3358884 · DOI
  16. Kawasaki E 2012 ZnT8 and type 1 diabetes Endocrine Journal 59 531 537 10.1507/endocrj.ej12-0069 22447136 · DOI
  17. Krezel A Maret W 2006 Zinc-buffering capacity of a eukaryotic cell at physiological pZn JBIC Journal of Biological Inorganic Chemistry 11 1049 1062 10.1007/s00775-006-0150-5 16924557 · DOI
  18. Lopez-Redondo ML Coudray N Zhang Z Alexopoulos J Stokes DL 2018 Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP PNAS 115 3042 3047 10.1073/pnas.1715051115 29507252 PMC5866550 · DOI
  19. Lu M Chai J Fu D 2009 Structural basis for autoregulation of the zinc transporter YiiP Nature Structural & Molecular Biology 16 1063 1067 10.1038/nsmb.1662 19749753 PMC2758918 · DOI
  20. Lu M Fu D 2007 Structure of the zinc transporter YiiP Science 317 1746 1748 10.1126/science.1143748 17717154 · DOI
  21. Maryon EB Molloy SA Ivy K Yu H Kaplan JH 2013 Rate and regulation of copper transport by human copper transporter 1 (hCTR1) Journal of Biological Chemistry 288 18035 18046 10.1074/jbc.M112.442426 23658018 PMC3689948 · DOI
  22. Mastronarde DN 2005 Automated electron microscope tomography using robust prediction of specimen movements Journal of Structural Biology 152 36 51 10.1016/j.jsb.2005.07.007 16182563 · DOI
  23. Merriman C Huang Q Rutter GA Fu D 2016 Lipid-tuned zinc transport activity of human ZnT8 protein correlates with risk for Type-2 diabetes Journal of Biological Chemistry 291 26950 26957 10.1074/jbc.M116.764605 27875315 PMC5207130 · DOI
  24. Ohana E Hoch E Keasar C Kambe T Yifrach O Hershfinkel M Sekler I 2009 Identification of the Zn2+ binding site and mode of operation of a mammalian Zn2+ transporter The Journal of Biological Chemistry 284 17677 17686 10.1074/jbc.M109.007203 19366695 PMC2719407 · DOI
  25. Parsons DS Hogstrand C Maret W 2018 The C-terminal cytosolic domain of the human zinc transporter ZnT8 and its diabetes risk variant The FEBS Journal 285 1237 1250 10.1111/febs.14402 29430817 PMC5947572 · DOI
  26. Pettersen EF Goddard TD Huang CC Couch GS Greenblatt DM Meng EC Ferrin TE 2004 UCSF chimera--a visualization system for exploratory research and analysis Journal of Computational Chemistry 25 1605 1612 10.1002/jcc.20084 15264254 · DOI
  27. Pound LD Sarkar SA Benninger RK Wang Y Suwanichkul A Shadoan MK Printz RL Oeser JK Lee CE Piston DW McGuinness OP Hutton JC Powell DR O'Brien RM 2009 Deletion of the mouse Slc30a8 gene encoding zinc transporter-8 results in impaired insulin secretion Biochemical Journal 421 371 376 10.1042/BJ20090530 19450229 PMC2929527 · DOI
  28. Prasad AS 2013 Discovery of human zinc deficiency: its impact on human health and disease Advances in Nutrition 4 176 190 10.3945/an.112.003210 23493534 PMC3649098 · DOI · Paper page
  29. Shusterman E Beharier O Shiri L Zarivach R Etzion Y Campbell CR Lee IH Okabayashi K Dinudom A Cook DI Katz A Moran A 2014 ZnT-1 extrudes zinc from mammalian cells functioning as a zn(2+)/H(+) exchanger Metallomics: Integrated Biometal Science 6 1656 1663 10.1039/c4mt00108g 24951051 · DOI
  30. Sievers F Wilm A Dineen D Gibson TJ Karplus K Li W Lopez R McWilliam H Remmert M Söding J Thompson JD Higgins DG 2011 Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega Molecular Systems Biology 7 539 10.1038/msb.2011.75 21988835 PMC3261699 · DOI
  31. Wenzlau JM Juhl K Yu L Moua O Sarkar SA Gottlieb P Rewers M Eisenbarth GS Jensen J Davidson HW Hutton JC 2007 The cation efflux transporter ZnT8 (Slc30A8) is a major autoantigen in human type 1 diabetes PNAS 104 17040 17045 10.1073/pnas.0705894104 17942684 PMC2040407 · DOI · Paper page
  32. Wijesekara N Dai FF Hardy AB Giglou PR Bhattacharjee A Koshkin V Chimienti F Gaisano HY Rutter GA Wheeler MB 2010 Beta cell-specific Znt8 deletion in mice causes marked defects in insulin processing, crystallisation and secretion Diabetologia 53 1656 1668 10.1007/s00125-010-1733-9 20424817 PMC6101216 · DOI
  33. Zhang K 2016 Gctf: real-time CTF determination and correction Journal of Structural Biology 193 1 12 10.1016/j.jsb.2015.11.003 26592709 PMC4711343 · DOI
  34. Zheng SQ Palovcak E Armache JP Verba KA Cheng Y Agard DA 2017 MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Nature Methods 14 331 332 10.1038/nmeth.4193 28250466 PMC5494038 · DOI
  35. Zivanov J Nakane T Forsberg BO Kimanius D Hagen WJ Lindahl E Scheres SH 2018 New tools for automated high-resolution cryo-EM structure determination in RELION-3 eLife 7 e42166 10.7554/eLife.42166 30412051 PMC6250425 · DOI

Cited by

Sorted by citations

Authors
Xue, J., Xie, T., Zeng, W., Jiang, Y., & Bai, X.-C.
Affiliations
  • Howard Hughes Medical Institute (US)
  • The University of Texas Southwestern Medical Center (US)
Corresponding author
  • Jiang, Youxing
  • Bai, Xiao-chen
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2020-07-29
Volume
9
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.58823
PMC
PMC7428307
OpenAlex
W3045541940
Cited by
78
References
4
Citations by year
2026: 5 · 2025: 13 · 2024: 12 · 2023: 18 · 2022: 9 · 2021: 17 · 2020: 4
FWCI
7.59
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institute of General Medical Sciences (R01GM136976, GM079179)
  • Welch Foundation (I-1944, I-1578)
  • Cancer Prevention and Research Institute of Texas (RP160082)
  • Howard Hughes Medical Institute
  • Virginia Murchison Linthicum Scholar in Medical Research
Topics
  • Health Sciences › Nursing › Nutrition and Dietetics › Trace Elements in Health
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
zinc transporter 8, zinc accumulation, insulin secretory granules, pancreatic beta cells, outward-facing conformation, inward-facing conformation, transmembrane domain, C-terminal domain, zinc binding site, alternating access, ion transport mechanism, protein dimer structure
MeSH terms
Protein Domains, Zinc Transporter 8, Amino Acid Sequence, Animals, Binding Sites, Humans, Models, Molecular, Protein Conformation, Zinc, Sequence Alignment, Antiporters, Cryoelectron Microscopy, HEK293 Cells

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