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- PDB-5vkq: Structure of a mechanotransduction ion channel Drosophila NOMPC i... -

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Basic information

Entry
Database: PDB / ID: 5vkq
TitleStructure of a mechanotransduction ion channel Drosophila NOMPC in nanodisc
ComponentsNo mechanoreceptor potential C isoform L
KeywordsMEMBRANE PROTEIN / Mechanotransduction Ion channel
Function / homology
Function and homology information


: / sensory perception of touch / detection of mechanical stimulus involved in sensory perception of touch / detection of mechanical stimulus involved in sensory perception / mechanosensory behavior / sensory perception of mechanical stimulus / response to auditory stimulus / mechanosensitive monoatomic ion channel activity / cation channel complex / locomotion ...: / sensory perception of touch / detection of mechanical stimulus involved in sensory perception of touch / detection of mechanical stimulus involved in sensory perception / mechanosensory behavior / sensory perception of mechanical stimulus / response to auditory stimulus / mechanosensitive monoatomic ion channel activity / cation channel complex / locomotion / ankyrin binding / startle response / monoatomic cation transport / monoatomic cation channel activity / sensory perception of sound / calcium channel activity / cilium / cellular response to mechanical stimulus / calcium ion transport / monoatomic ion channel activity / dendrite / neuronal cell body
Similarity search - Function
Domain of unknown function DUF3447 / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / No mechanoreceptor potential C isoform L
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsJin, P. / Bulkley, D. / Guo, Y. / Zhang, W. / Guo, Z. / Huynh, W. / Wu, S. / Meltzer, S. / Chen, T. / Jan, L.Y. ...Jin, P. / Bulkley, D. / Guo, Y. / Zhang, W. / Guo, Z. / Huynh, W. / Wu, S. / Meltzer, S. / Chen, T. / Jan, L.Y. / Jan, Y.-N. / Cheng, Y.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS069229 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5R37NS040929 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R35NS097227 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
CitationJournal: Nature / Year: 2017
Title: Electron cryo-microscopy structure of the mechanotransduction channel NOMPC.
Authors: Peng Jin / David Bulkley / Yanmeng Guo / Wei Zhang / Zhenhao Guo / Walter Huynh / Shenping Wu / Shan Meltzer / Tong Cheng / Lily Yeh Jan / Yuh-Nung Jan / Yifan Cheng /
Abstract: Mechanosensory transduction for senses such as proprioception, touch, balance, acceleration, hearing and pain relies on mechanotransduction channels, which convert mechanical stimuli into electrical ...Mechanosensory transduction for senses such as proprioception, touch, balance, acceleration, hearing and pain relies on mechanotransduction channels, which convert mechanical stimuli into electrical signals in specialized sensory cells. How force gates mechanotransduction channels is a central question in the field, for which there are two major models. One is the membrane-tension model: force applied to the membrane generates a change in membrane tension that is sufficient to gate the channel, as in the bacterial MscL channel and certain eukaryotic potassium channels. The other is the tether model: force is transmitted via a tether to gate the channel. The transient receptor potential (TRP) channel NOMPC is important for mechanosensation-related behaviours such as locomotion, touch and sound sensation across different species including Caenorhabditis elegans, Drosophila and zebrafish. NOMPC is the founding member of the TRPN subfamily, and is thought to be gated by tethering of its ankyrin repeat domain to microtubules of the cytoskeleton. Thus, a goal of studying NOMPC is to reveal the underlying mechanism of force-induced gating, which could serve as a paradigm of the tether model. NOMPC fulfils all the criteria that apply to mechanotransduction channels and has 29 ankyrin repeats, the largest number among TRP channels. A key question is how the long ankyrin repeat domain is organized as a tether that can trigger channel gating. Here we present a de novo atomic structure of Drosophila NOMPC determined by single-particle electron cryo-microscopy. Structural analysis suggests that the ankyrin repeat domain of NOMPC resembles a helical spring, suggesting its role of linking mechanical displacement of the cytoskeleton to the opening of the channel. The NOMPC architecture underscores the basis of translating mechanical force into an electrical signal within a cell.
History
DepositionApr 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Data collection / Experimental preparation
Category: em_sample_support / em_software / pdbx_audit_support
Item: _em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.6Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: No mechanoreceptor potential C isoform L
B: No mechanoreceptor potential C isoform L
C: No mechanoreceptor potential C isoform L
D: No mechanoreceptor potential C isoform L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)779,40436
Polymers755,9154
Non-polymers23,48932
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53410 Å2
ΔGint-453 kcal/mol
Surface area245430 Å2

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Components

#1: Protein
No mechanoreceptor potential C isoform L / No mechanoreceptor potential C / isoform E


Mass: 188978.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: nompC, CG11020, Dmel_CG11020 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: E0A9E1
#2: Chemical...
ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Dipalmitoylphosphatidylcholine


Mass: 734.039 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C40H80NO8P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.754893 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 8.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMBicineC6H13NO41
2500 mMSaltNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acidC10H16N2O81
SpecimenConc.: 3.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: sample solubilized in nanodisc
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 92 % / Chamber temperature: 20 K
Details: 2.5 sec blot, -1 offset, whatman #1 filter paper on front side, plastic on back side

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 X / Calibrated magnification: 41132 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1500 nm / Calibrated defocus min: -1400 nm / Calibrated defocus max: -3300 nm / Cs: 2.1 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER
Temperature (max): 83 K / Temperature (min): 83 K
Image recordingAverage exposure time: 8 sec. / Electron dose: 54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1873
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 2-40

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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
2SerialEM3.4image acquisition
4Gctf1.06CTF correction
7Coot0.8.7model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIXdev-2608model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 190879
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175314 / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingB value: 125.7 / Protocol: AB INITIO MODEL / Space: REAL

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