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- EMDB-8702: Structure of a mechanotransduction ion channel Drosophila NOMPC i... -

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Basic information

Entry
Database: EMDB / ID: EMD-8702
TitleStructure of a mechanotransduction ion channel Drosophila NOMPC in nanodisc
Map dataan ion channel in nano disc -- final sharpened map
Sample
  • Complex: Tetrameric channel
    • Protein or peptide: No mechanoreceptor potential C isoform L
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
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
No mechanoreceptor potential C isoform L
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsJin P
Funding support United States, 7 items
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, 2017-
Header (metadata) releaseJun 28, 2017-
Map releaseJun 28, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5vkq
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8702.png

Downloads & links

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Map

FileDownload / File: emd_8702.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationan ion channel in nano disc -- final sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 400 pix.
= 486.24 Å		1.22 Å/pix.
x 400 pix.
= 486.24 Å		1.22 Å/pix.
x 400 pix.
= 486.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0 / Movie #1: 10
Minimum - Maximum-27.666853 - 60.020862999999999
Average (Standard dev.)-0.000000000243273 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 486.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21561.21561.2156
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z486.240486.240486.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-27.66760.021-0.000

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Supplemental data

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Additional map: an ion channel in nano disc -- final unsharpened map

Fileemd_8702_additional_1.map
Annotationan ion channel in nano disc -- final unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: an ion channel in nano disc -- class 1

Fileemd_8702_additional_2.map
Annotationan ion channel in nano disc -- class 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: an ion channel in nano disc -- class 2

Fileemd_8702_additional_3.map
Annotationan ion channel in nano disc -- class 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: an ion channel in nano disc -- class 3

Fileemd_8702_additional_4.map
Annotationan ion channel in nano disc -- class 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: an ion channel in nano disc -- half volume 1

Fileemd_8702_half_map_1.map
Annotationan ion channel in nano disc -- half volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: an ion channel in nano disc -- half volume 2

Fileemd_8702_half_map_2.map
Annotationan ion channel in nano disc -- half volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric channel

EntireName: Tetrameric channel
Components
  • Complex: Tetrameric channel
    • Protein or peptide: No mechanoreceptor potential C isoform L
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

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Supramolecule #1: Tetrameric channel

SupramoleculeName: Tetrameric channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 754.893 KDa

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Macromolecule #1: No mechanoreceptor potential C isoform L

MacromoleculeName: No mechanoreceptor potential C isoform L / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 188.978734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQPRGGRGG GRGGGVGRKT PSSLTGPPDE SATPSERATP ASKADSDPKD DSSSNGDKKD MDLFPAPKPP SAGASIRDTA NKVLGLAMK SEWTPIEAEL KKLEKYVANV GEDGNHIPLA GVHDMNTGMT PLMYATKDNK TAIMDRMIEL GADVGARNND N YNVLHIAA ...String:
MSQPRGGRGG GRGGGVGRKT PSSLTGPPDE SATPSERATP ASKADSDPKD DSSSNGDKKD MDLFPAPKPP SAGASIRDTA NKVLGLAMK SEWTPIEAEL KKLEKYVANV GEDGNHIPLA GVHDMNTGMT PLMYATKDNK TAIMDRMIEL GADVGARNND N YNVLHIAA MYSREDVVKL LLTKRGVDPF STGGSRSQTA VHLVSSRQTG TATNILRALL AAAGKDIRLK ADGRGKIPLL LA VESGNQS MCRELLAAQT AEQLKATTAN GDTALHLAAR RRDVDMVRIL VDYGTNVDTQ NGEGQTPLHI AAAEGDEALL KYF YGVRAS ASIADNQDRT PMHLAAENGH AHVIEILADK FKASIFERTK DGSTLMHIAS LNGHAECATM LFKKGVYLHM PNKD GARSI HTAAAYGHTG IINTLLQKGE KVDVTTNDNY TALHIAVESA KPAVVETLLG FGADVHVRGG KLRETPLHIA ARVKD GDRC ALMLLKSGAS PNLTTDDCLT PVHVAARHGN LATLMQLLED EGDPLYKSNT GETPLHMACR ACHPDIVRHL IETVKE KHG PDKATTYINS VNEDGATALH YTCQITKEEV KIPESDKQIV RMLLENGADV TLQTKTALET AFHYCAVAGN NDVLMEM IS HMNPTDIQKA MNRQSSVGWT PLLIACHRGH MELVNNLLAN HARVDVFDTE GRSALHLAAE RGYLHVCDAL LTNKAFIN S KSRVGRTALH LAAMNGFTHL VKFLIKDHNA VIDILTLRKQ TPLHLAAASG QMEVCQLLLE LGANIDATDD LGQKPIHVA AQNNYSEVAK LFLQQHPSLV NATSKDGNTC AHIAAMQGSV KVIEELMKFD RSGVISARNK LTDATPLQLA AEGGHADVVK ALVRAGASC TEENKAGFTA VHLAAQNGHG QVLDVLKSTN SLRINSKKLG LTPLHVAAYY GQADTVRELL TSVPATVKSE T PTGQSLFG DLGTESGMTP LHLAAFSGNE NVVRLLLNSA GVQVDAATIE NGYNPLHLAC FGGHMSVVGL LLSRSAELLQ SQ DRNGRTG LHIAAMHGHI QMVEILLGQG AEINATDRNG WTPLHCAAKA GHLEVVKLLC EAGASPKSET NYGCAAIWFA ASE GHNEVL RYLMNKEHDT YGLMEDKRFV YNLMVVSKNH NNKPIQEFVL VSPAPVDTAA KLSNIYIVLS TKEKERAKDL VAAG KQCEA MATELLALAA GSDSAGKILQ ATDKRNVEFL DVLIENEQKE VIAHTVVQRY LQELWHGSLT WASWKILLLL VAFIV CPPV WIGFTFPMGH KFNKVPIIKF MSYLTSHIYL MIHLSIVGIT PIYPVLRLSL VPYWYEVGLL IWLSGLLLFE LTNPSD KSG LGSIKVLVLL LGMAGVGVHV SAFLFVSKEY WPTLVYCRNQ CFALAFLLAC VQILDFLSFH HLFGPWAIII GDLLKDL AR FLAVLAIFVF GFSMHIVALN QSFANFSPED LRSFEKKNRN RGYFSDVRMH PINSFELLFF AVFGQTTTEQ TQVDKIKN V ATPTQPYWVE YLFKIVFGIY MLVSVVVLIQ LLIAMMSDTY QRIQAQSDIE WKFGLSKLIR NMHRTTTAPS PLNLVTTWF MWIVEKVKAR MKKKKRPSLV QMMGIRQASP RTKAGAKWLS KIKKDSVALS QVHLSPLGSQ ASFSQANQNR IENVADWEAI AKKYRALVG DEEGGSLKDS DAESGSQEGS GGQQPPAQVG RRAIKATLAD TTK

UniProtKB: No mechanoreceptor potential C isoform L

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Macromolecule #2: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 2 / Number of copies: 32 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Dipalmitoylphosphatidylcholine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.4 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4Bicine
500.0 mMNaClSodium chlorideSalt
1.0 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 92 % / Chamber temperature: 20 K / Instrument: GATAN CRYOPLUNGE 3
Details: 2.5 sec blot, -1 offset, whatman #1 filter paper on front side, plastic on back side.
Detailssample solubilized in nanodisc

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: -3.3000000000000003 µm / Calibrated defocus min: -1.4000000000000001 µm / Calibrated magnification: 41132 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.1 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 83.0 K / Max: 83.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 1873 / Average exposure time: 8.0 sec. / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 190879
Startup modelType of model: OTHER / Details: SIMPLE PRIME used to generate initial model
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Avg.num./class: 31600 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 175314

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 125.7
Output model

PDB-5vkq:
Structure of a mechanotransduction ion channel Drosophila NOMPC in nanodisc

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