IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-40532-2.html
   My bibliography  Save this article

Structure and regulation of full-length human leucine-rich repeat kinase 1

Author

Listed:
  • Riley D. Metcalfe

    (Center for Structural Biology, Center for Cancer Research, National Cancer Institute)

  • Juliana A. Martinez Fiesco

    (Center for Structural Biology, Center for Cancer Research, National Cancer Institute)

  • Luis Bonet-Ponce

    (Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health)

  • Jillian H. Kluss

    (Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health)

  • Mark R. Cookson

    (Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health)

  • Ping Zhang

    (Center for Structural Biology, Center for Cancer Research, National Cancer Institute)

Abstract

The human leucine-rich repeat kinases (LRRKs), LRRK1 and LRRK2 are large and unusually complex multi-domain kinases, which regulate fundamental cellular processes and have been implicated in human disease. Structures of LRRK2 have recently been determined, but the structure and molecular mechanisms regulating the activity of the LRRK1 as well as differences in the regulation of LRRK1 and LRRK2 remain unclear. Here, we report a cryo-EM structure of the LRRK1 monomer and a lower-resolution cryo-EM map of the LRRK1 dimer. The monomer structure, in which the kinase is in an inactive conformation, reveals key interdomain interfaces that control kinase activity as we validate experimentally. Both the LRRK1 monomer and dimer are structurally distinct compared to LRRK2. Overall, our results provide structural insights into the activation of the human LRRKs, which advance our understanding of their physiological and pathological roles.

Suggested Citation

  • Riley D. Metcalfe & Juliana A. Martinez Fiesco & Luis Bonet-Ponce & Jillian H. Kluss & Mark R. Cookson & Ping Zhang, 2023. "Structure and regulation of full-length human leucine-rich repeat kinase 1," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40532-2
    DOI: 10.1038/s41467-023-40532-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-40532-2
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-40532-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Hiroshi Hanafusa & Kouki Ishikawa & Shin Kedashiro & Tsukasa Saigo & Shun-ichiro Iemura & Tohru Natsume & Masayuki Komada & Hiroshi Shibuya & Atsuki Nara & Kunihiro Matsumoto, 2011. "Leucine-rich repeat kinase LRRK1 regulates endosomal trafficking of the EGF receptor," Nature Communications, Nature, vol. 2(1), pages 1-12, September.
    2. Tristan Bepler & Kotaro Kelley & Alex J. Noble & Bonnie Berger, 2020. "Topaz-Denoise: general deep denoising models for cryoEM and cryoET," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    3. C. K. Deniston & J. Salogiannis & S. Mathea & D. M. Snead & I. Lahiri & M. Matyszewski & O. Donosa & R. Watanabe & J. Böhning & A. K. Shiau & S. Knapp & E. Villa & S. L. Reck-Peterson & A. E. Leschzin, 2020. "Structure of LRRK2 in Parkinson’s disease and model for microtubule interaction," Nature, Nature, vol. 588(7837), pages 344-349, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yun-Tao Liu & Heng Zhang & Hui Wang & Chang-Lu Tao & Guo-Qiang Bi & Z. Hong Zhou, 2022. "Isotropic reconstruction for electron tomography with deep learning," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Xinyu Zhang & Tianfang Zhao & Jiansheng Chen & Yuan Shen & Xueming Li, 2022. "EPicker is an exemplar-based continual learning approach for knowledge accumulation in cryoEM particle picking," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Qiansheng Liang & Gamma Chi & Leonardo Cirqueira & Lianteng Zhi & Agostino Marasco & Nadia Pilati & Martin J. Gunthorpe & Giuseppe Alvaro & Charles H. Large & David B. Sauer & Werner Treptow & Manuel , 2024. "The binding and mechanism of a positive allosteric modulator of Kv3 channels," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Luka Bacic & Guillaume Gaullier & Jugal Mohapatra & Guanzhong Mao & Klaus Brackmann & Mikhail Panfilov & Glen Liszczak & Anton Sabantsev & Sebastian Deindl, 2024. "Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Sriram Aiyer & Philip R. Baldwin & Shi Min Tan & Zelin Shan & Juntaek Oh & Atousa Mehrani & Marianne E. Bowman & Gordon Louie & Dario Oliveira Passos & Selena Đorđević-Marquardt & Mario Mietzsch & Jos, 2024. "Overcoming resolution attenuation during tilted cryo-EM data collection," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    6. Benjamin C. Creekmore & Kathryn Kixmoeller & Ben E. Black & Edward B. Lee & Yi-Wei Chang, 2024. "Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Felix J. Metzner & Simon J. Wenzl & Michael Kugler & Stefan Krebs & Karl-Peter Hopfner & Katja Lammens, 2022. "Mechanistic understanding of human SLFN11," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    8. Kathryn H. Gunn & Saskia B. Neher, 2023. "Structure of dimeric lipoprotein lipase reveals a pore adjacent to the active site," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Fengfeng Niu & Lingxuan Li & Lei Wang & Jinman Xiao & Shun Xu & Yong Liu & Leishu Lin & Cong Yu & Zhiyi Wei, 2024. "Autoinhibition and activation of myosin VI revealed by its cryo-EM structure," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. Kotaro Kelley & Ashleigh M. Raczkowski & Oleg Klykov & Pattana Jaroenlak & Daija Bobe & Mykhailo Kopylov & Edward T. Eng & Gira Bhabha & Clinton S. Potter & Bridget Carragher & Alex J. Noble, 2022. "Waffle Method: A general and flexible approach for improving throughput in FIB-milling," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    11. Ryo Nagao & Koji Kato & Tasuku Hamaguchi & Yoshifumi Ueno & Naoki Tsuboshita & Shota Shimizu & Miyu Furutani & Shigeki Ehira & Yoshiki Nakajima & Keisuke Kawakami & Takehiro Suzuki & Naoshi Dohmae & S, 2023. "Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    12. J. Josephine Botsch & Roswitha Junker & Michèle Sorgenfrei & Patricia P. Ogger & Luca Stier & Susanne Gronau & Peter J. Murray & Markus A. Seeger & Brenda A. Schulman & Bastian Bräuning, 2024. "Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    13. Pablo Gallego & Maria-Jose Garcia-Bonete & Sergio Trillo-Muyo & Christian V. Recktenwald & Malin E. V. Johansson & Gunnar C. Hansson, 2023. "The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    14. Melanie Arndt & Carolina Alvadia & Monique S. Straub & Vanessa Clerico Mosina & Cristina Paulino & Raimund Dutzler, 2022. "Structural basis for the activation of the lipid scramblase TMEM16F," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    15. Alexander Domnick & Christian Winter & Lukas Sušac & Leon Hennecke & Mario Hensen & Nicole Zitzmann & Simon Trowitzsch & Christoph Thomas & Robert Tampé, 2022. "Molecular basis of MHC I quality control in the peptide loading complex," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    16. Haonan Zhang & Yan Li & Yanan Liu & Dongyu Li & Lin Wang & Kai Song & Keyan Bao & Ping Zhu, 2023. "A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    17. Dohyun Im & Jun-ichi Kishikawa & Yuki Shiimura & Hiromi Hisano & Akane Ito & Yoko Fujita-Fujiharu & Yukihiko Sugita & Takeshi Noda & Takayuki Kato & Hidetsugu Asada & So Iwata, 2023. "Structural insights into the agonists binding and receptor selectivity of human histamine H4 receptor," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    18. Atsushi Yamagata & Yoshiko Murata & Kosuke Namba & Tohru Terada & Shuya Fukai & Mikako Shirouzu, 2022. "Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    19. Hongcheng Fan & Bo Wang & Yan Zhang & Yun Zhu & Bo Song & Haijin Xu & Yujia Zhai & Mingqiang Qiao & Fei Sun, 2021. "A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI," Nature Communications, Nature, vol. 12(1), pages 1-13, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40532-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.