6OT2

Structure of the TRPV3 K169A sensitized mutant in apo form at 4.1 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Regulatory switch at the cytoplasmic interface controls TRPV channel gating.

Zubcevic, L.Borschel, W.F.Hsu, A.L.Borgnia, M.J.Lee, S.Y.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.47746
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Temperature-sensitive transient receptor potential vanilloid (thermoTRPV) channels are activated by ligands and heat, and are involved in various physiological processes. ThermoTRPV channels possess a large cytoplasmic ring consisting of N-terminal a ...

    Temperature-sensitive transient receptor potential vanilloid (thermoTRPV) channels are activated by ligands and heat, and are involved in various physiological processes. ThermoTRPV channels possess a large cytoplasmic ring consisting of N-terminal ankyrin repeat domains (ARD) and C-terminal domains (CTD). The cytoplasmic inter-protomer interface is unique and consists of a CTD coiled around a b-sheet which makes contacts with the neighboring ARD. Despite much existing evidence that the cytoplasmic ring is important for thermoTRPV function, the mechanism by which this unique structure is involved in thermoTRPV gating has not been clear. Here we present cryo-EM and electrophysiological studies which demonstrate that TRPV3 gating involves large rearrangements at the cytoplasmic inter-protomer interface and that this motion triggers coupling between cytoplasmic and transmembrane domains, priming the channel for opening. Furthermore, our studies unveil the role of this interface in the distinct biophysical and physiological properties of individual thermoTRPV subtypes.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea. Electronic address: chahong@korea.ac.kr.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.,Helmholtz Centre for Infection Research , 38124 Braunschweig , Germany.,Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand.,Department of Biology, Southern University of Science and Technology of China, Shenzhen, 518055 Guangdong, China.,Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133, Milano, Italy. emilio.parisini@iit.it.,Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,School of Biological Sciences , Nanyang Technological University , 639798 Singapore.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Departments of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, United States.,Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy. alfonso.gautieri@polimi.it.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands.,Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.,Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan tanaka.hiroshi@chugai-pharm.co.jp.,Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada.,Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.,Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA. Electronic address: qunliu@bnl.gov.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands.,Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133, Milano, Italy.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.,Manufacturing, Commonwealth Scientific and Industrial Research Organization (CSIRO) , Clayton , Vic 3168 , Australia.,Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.,Department of Biophysics, Bose Institute, Kolkata, 700054, India. Electronic address: bhunia@jcbose.ac.in.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Biotechnology, IIT Madras, Chennai, 600036, India.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France.,SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Department of Biochemistry, Duke University School of Medicine, Durham, United States.,Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. kwmiller@mgh.harvard.edu.,Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,School of Life Science , Huizhou University , Huizhou 516007 , China.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand emily.parker@vuw.ac.nz g.b.jameson@massey.ac.nz.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Technical University Darmstadt , Alarich-Weiss-Straße 4 , 64287 Darmstadt , Germany.,Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, China; jacobsen@ucla.edu jmdu@sibs.ac.cn.,NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, Netherlands.,MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.,Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan hiroaki.mitsuya2@nih.gov.,National Institute of Biological Sciences, Beijing, China.,Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institute , 5232 Villigen , Switzerland.,Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany goerlich@mpibpc.mpg.de.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095; jacobsen@ucla.edu jmdu@sibs.ac.cn.,Department of Infectious Diseases and Microbiology , University of Lübeck , 23562 Lübeck , Germany.,Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea.,AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. shaofeng@nibs.ac.cn.,School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nisimasu@bs.s.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Max Planck Institute of Biochemistry , 82152 Martinsried , Germany.,Department of Biophysics, Bose Institute, Kolkata, 700054, India.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.,Institute of Oceanography, Minjiang University, 350108 Fuzhou, China.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China. dhlin@xmu.edu.cn.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA.,Dipartimento di Scienze della Terra , Università di Pisa , via Santa Maria 53 , 56126 Pisa , Italy.,Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea.,Laboratory Molecular and Cellular Signaling, Department Cellular and Molecular Medicine, Campus Gasthuisberg O/N-I Bus 802, Herestraat 49 3000 Leuven, Belgium.,Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,School of Nanoscience and Technology, IIT Kharagpur, Kharagpur, 721302, India. Electronic address: anupam.midya@iitkgp.ac.in.,Division of Molecular Medicine, Bose Institute, Kolkata, 700054, India.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. s.s.virdee@dundee.ac.uk.,D3-PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.,Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.,Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , 80804 Munich , Germany.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. simonasm@mrc-lmb.cam.ac.uk.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.,Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand.,University of Chinese Academy of Sciences , No. 19 Yuquan Road , Beijing 100049 , China.,Institute of Technology, University of Tartu, 50411 Tartu, Estonia.,School of Chemistry, National University of Ireland, University Road, Galway, Ireland.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.,NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.,School of Biological Sciences & Maurice Wilkins Centre , University of Auckland , Auckland 1010 , New Zealand.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA mr@purdue.edu.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Institute for Genetics, University of Cologne, Cologne, Germany.,Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 90187 Umeå, Sweden.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences , Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences ; Guangzhou Medical University, Guangzhou 510530 , China.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary.,Experimental Retrovilogy Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Pharmaceutical Sciences , Jilin University , No.1266 Fujin Road , Chaoyang District, Changchun , Jilin 130021 , China.,National Institute of Biological Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.,University of Lübeck , 23562 Lübeck , Germany.,School of Nanoscience and Technology, IIT Kharagpur, Kharagpur, 721302, India.,Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada.,Centro de Química Estrutural, Instituto Superior Técnico , Universidade de Lisboa , Av. Rovisco Pais 1 , 1049-001 Lisboa , Portugal.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette , France.,Structural Genomics Consortium, University of Toronto , 101 College Street, Toronto, ON M5G 1L7, Canada.,University of Chinese Academy of Sciences, 100049 Beijing, China.,Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.,Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MA 21224, USA. Electronic address: lei.shi2@nih.gov.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. radu@mrc-lmb.cam.ac.uk.,Department of Pharmacy, Uppsala University, SE-75232, Uppsala, Sweden; Department of Pharmacy, University of Copenhagen, DK-2100, Copenhagen, Denmark. Electronic address: martin.malmsten@farmaci.uu.se.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand.,Department of Physics, IIT Kharagpur, Kharagpur, 721302, India.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530 , China.,Technische Universität Braunschweig , 38106 Braunschweig , Germany.,School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; daniel.wilson@chemie.uni-hamburg.de.,National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, China.,McGovern Institute for Brain Research, Cambridge, MA 02139, USA.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095.,Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.,Beijing Mingde Zhengkang Technologies Co., Ltd., Beijing, China.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA.,Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA. Electronic address: mq2102@cumc.columbia.edu.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL) , Guangzhou 510530 , China.,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transient receptor potential cation channel subfamily V member 3
A, B, D, C
734Homo sapiensMutation(s): 1 
Gene Names: TRPV3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
TRPV3 transient receptor potential channel in apo conformation
Find proteins for Q8NET8 (Homo sapiens)
Go to Gene View: TRPV3
Go to UniProtKB:  Q8NET8
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesR35NS097241
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesZIC ES103326

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release