Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn2+ uptake into the Golgi apparatus

被引:16
作者
Bui, Han Ba [1 ,2 ]
Watanabe, Satoshi [1 ,2 ,3 ]
Nomura, Norimichi [4 ]
Liu, Kehong [4 ]
Uemura, Tomoko [4 ]
Inoue, Michio [1 ]
Tsutsumi, Akihisa [5 ]
Fujita, Hiroyuki [6 ]
Kinoshita, Kengo [7 ,8 ]
Kato, Yukinari [9 ]
Iwata, So [4 ]
Kikkawa, Masahide [5 ]
Inaba, Kenji [1 ,2 ,3 ,10 ,11 ]
机构
[1] Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai, Miyagi 9808577, Japan
[2] Tohoku Univ, Grad Sch Life Sci, Dept Mol & Chem Life Sci, Sendai, Miyagi 9808577, Japan
[3] Tohoku Univ, Grad Sch Sci, Dept Chem, Sendai, Miyagi 9808578, Japan
[4] Kyoto Univ, Grad Sch Med, Dept Cell Biol, Kyoto 6068501, Japan
[5] Univ Tokyo, Grad Sch Med, 7-3-1 Hongo,Bunkyo Ku, Tokyo 1130033, Japan
[6] Canon Med Syst Corp, Adv Res Lab, Otawara 3248550, Japan
[7] Tohoku Univ, Grad Sch Informat Sci, Dept Syst Bioinformat, Sendai, Miyagi 9808579, Japan
[8] Tohoku Univ, Dept Integrat Genom, Tohoku Med Megabank Org, Sendai, Miyagi 9808573, Japan
[9] Tohoku Univ, Grad Sch Med, Sendai 9808575, Japan
[10] Kyushu Univ, Med Inst Bioregulat, Fukuoka 8128582, Japan
[11] Japan Agcy Med Res & Dev AMED, Core Res Evolut Sci & Technol CREST, Tokyo, Japan
关键词
HISTIDINE-RICH LOOP; ARABIDOPSIS-THALIANA; PROTEINS; VISUALIZATION; CONFORMATION; TOOLS;
D O I
10.1038/s41467-023-40521-5
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
ZnT7 is a Golgi-localized Zn2 + /H+ antiporter. Here the authors present the cryo-EM structures of human ZnT7 in Zn2 + -bound and unbound forms, shedding light on its mechanism of Zn2+ transport. Zinc ions (Zn2+) are vital to most cells, with the intracellular concentrations of Zn2+ being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein present the 2.2-3.1 & ANGS;-resolution cryo-EM structures of a Golgi-localized human Zn2+/H+ antiporter ZnT7 (hZnT7) in Zn2+-bound and unbound forms. Cryo-EM analyses show that hZnT7 exists as a dimer via tight interactions in both the cytosolic and transmembrane (TM) domains of two protomers, each of which contains a single Zn2+-binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn2+ entry in the inward-facing conformation and widens the luminal cavity for Zn2+ release in the outward-facing conformation. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 binds two Zn2+ ions, seemingly facilitating Zn2+ recruitment to the TM metal transport pathway. These structures permit mechanisms of hZnT7-mediated Zn2+ uptake into the Golgi to be proposed.
引用
收藏
页数:16
相关论文
共 46 条
[1]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[2]   Zinc homeostasis governed by Golgi-resident ZnT family members regulates ERp44-mediated proteostasis at the ER-Golgi interface [J].
Amagai, Yuta ;
Yamada, Momo ;
Kowada, Toshiyuki ;
Watanabe, Tomomi ;
Du, Yuyin ;
Liu, Rong ;
Naramoto, Satoshi ;
Watanabe, Satoshi ;
Kyozuka, Junko ;
Anelli, Tiziana ;
Tempio, Tiziana ;
Sitia, Roberto ;
Mizukami, Shin ;
Inaba, Kenji .
NATURE COMMUNICATIONS, 2023, 14 (01)
[3]   Counting the zinc-proteins encoded in the human genome [J].
Andreini, C ;
Banci, L ;
Bertini, I ;
Rosato, A .
JOURNAL OF PROTEOME RESEARCH, 2006, 5 (01) :196-201
[4]  
Asarnow Daniel, 2019, Zenodo
[5]   Recent developments in the CCP-EM software suite [J].
Burnley, Tom ;
Palmer, Colin M. ;
Winn, Martyn .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2017, 73 :469-477
[6]  
Chi ZH, 2009, HISTOL HISTOPATHOL, V24, P25, DOI 10.14670/HH-24.25
[7]   Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy [J].
Coudray, Nicolas ;
Valvo, Salvatore ;
Hu, Minghui ;
Lasala, Ralph ;
Kim, Changki ;
Vink, Martin ;
Zhou, Ming ;
Provasi, Davide ;
Filizola, Marta ;
Tao, Juoehi ;
Fang, Jia ;
Penczek, Pawel A. ;
Ubarretxena-Belandia, Iban ;
Stokes, David L. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (06) :2140-2145
[8]   Time-resolved cryo-EM using Spotiton [J].
Dandey, Venkata P. ;
Budell, William C. ;
Wei, Hui ;
Bobe, Daija ;
Maruthi, Kashyap ;
Kopylov, Mykhailo ;
Eng, Edward T. ;
Kahn, Peter A. ;
Hinshaw, Jenny E. ;
Kundu, Nidhi ;
Nimigean, Crina M. ;
Fan, Chen ;
Sukomon, Nattakan ;
Darst, Seth A. ;
Saecker, Ruth M. ;
Chen, James ;
Malone, Brandon ;
Potter, Clinton S. ;
Carragher, Bridget .
NATURE METHODS, 2020, 17 (09) :897-+
[9]   MolProbity: all-atom contacts and structure validation for proteins and nucleic acids [J].
Davis, Ian W. ;
Leaver-Fay, Andrew ;
Chen, Vincent B. ;
Block, Jeremy N. ;
Kapral, Gary J. ;
Wang, Xueyi ;
Murray, Laura W. ;
Arendall, W. Bryan, III ;
Snoeyink, Jack ;
Richardson, Jane S. ;
Richardson, David C. .
NUCLEIC ACIDS RESEARCH, 2007, 35 :W375-W383
[10]  
DeLano W.L., 2020, The PYMOL Molecular Graphics System