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- EMDB-20499: Cryo-EM Structure of Thermo-Sensitive TRP Channel TRP1 from the A... -

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Basic information

Entry
Database: EMDB / ID: EMD-20499
TitleCryo-EM Structure of Thermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas reinhardtii in Nanodiscs
Map dataThermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas reinhardtii in nanodiscs
Sample
  • Complex: crTRP1 in nanodiscs
    • Protein or peptide: TRP-like ion channel
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate
Function / homology
Function and homology information


store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / regulation of cytosolic calcium ion concentration / calcium ion transmembrane transport / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
TRP-like ion channel
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsMcGoldrick LL / Singh AK / Sobolevsky AI
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA206573 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the thermo-sensitive TRP channel TRP1 from the alga Chlamydomonas reinhardtii.
Authors: Luke L McGoldrick / Appu K Singh / Lusine Demirkhanyan / Ting-Yu Lin / Ryan G Casner / Eleonora Zakharian / Alexander I Sobolevsky /
Abstract: Algae produce the largest amount of oxygen on earth and are invaluable for human nutrition and biomedicine, as well as for the chemical industry, energy production and agriculture. The mechanisms by ...Algae produce the largest amount of oxygen on earth and are invaluable for human nutrition and biomedicine, as well as for the chemical industry, energy production and agriculture. The mechanisms by which algae can detect and respond to changes in their environments can rely on membrane receptors, including TRP ion channels. Here we present a 3.5-Å resolution cryo-EM structure of the transient receptor potential (TRP) channel crTRP1 from the alga Chlamydomonas reinhardtii that opens in response to increased temperature and is positively regulated by the membrane lipid PIP. The structure of crTRP1 significantly deviates from the structures of other TRP channels and has a unique 2-fold symmetrical rose-shape architecture with elbow domains and ankyrin repeat domains submerged and dipping into the membrane, respectively. Our study provides a structure of a TRP channel from a micro-organism and a structural framework for better understanding algae biology and TRP channel evolution.
History
DepositionJul 22, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseSep 25, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0169
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0169
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pw5
  • Surface level: 0.0169
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20499.png

Downloads & links

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Map

FileDownload / File: emd_20499.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas reinhardtii in nanodiscs
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.0169 / Movie #1: 0.0169
Minimum - Maximum-0.09994492 - 0.15298614
Average (Standard dev.)0.0011471657 (±0.0077296174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 190.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.950.950.95
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z190.000190.000190.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1548552
NX/NY/NZ198170217
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1000.1530.001

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Supplemental data

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Sample components

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Entire : crTRP1 in nanodiscs

EntireName: crTRP1 in nanodiscs
Components
  • Complex: crTRP1 in nanodiscs
    • Protein or peptide: TRP-like ion channel
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate

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Supramolecule #1: crTRP1 in nanodiscs

SupramoleculeName: crTRP1 in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: TRP-like ion channel

MacromoleculeName: TRP-like ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 99.538742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVAPAPASG QPGGGSKKPS DYGCQLHYKH ARVVEPESTT DDGMKRLKDV GDKGTLITAA ELGLVDKYRD LKRAGQDILT CDWPYHYSS ILYACYGNQY KILQMVEREF VGSTQELTAM HTTRCWVGKN SAMVAAYQGH LETMLYIIDL DMQGKFTEDL F KQRDVMGK ...String:
MKVAPAPASG QPGGGSKKPS DYGCQLHYKH ARVVEPESTT DDGMKRLKDV GDKGTLITAA ELGLVDKYRD LKRAGQDILT CDWPYHYSS ILYACYGNQY KILQMVEREF VGSTQELTAM HTTRCWVGKN SAMVAAYQGH LETMLYIIDL DMQGKFTEDL F KQRDVMGK NAMMWAASQG HTDTIEVLLV RSLYRLLPED CADPLVLKTR WKLVSLLADL ASHCRDYDPG CSRSFFQEVL AS IKYDPVE GARQEEAAAA GGGGSAREGA ALHEPTWGVD DGEEEERRHG VKHSDLVGKS AASTTAAAAA GGKTASGKPG EPG GGGAVK LKDVHITVRT LQGVIVSAYR AGMNCMGVIM YCQSLLQQAR YFDDLVAQLT AWEVKLLDTC RNKQEVQAIL APTE DDPSE PVGYALATFD KAFLSHKFVQ QIFTEKWDTM GVTDYTKSLF GVVWGGCSLV VAFAAWATIC PLVVVARSFL SPVQD FMMR GKVIVDSRFP WHVPLYRWLL TQCALITFTV LLSYLVFSFD PSDPVPASVA PLNTFLAVWC AAILVDEVQE YVEEGR AEY MSSGWNVMDV TMALSYILHY ILRIIAVRVT DNLNILLVVN DLLAAAALMA WFRMVSVFEL SSAIGPLIQM MKQMLIK DV TRFALLVLVI LLGFSVGMEA LFQEACIERD PTTNECTKYT SWGYDWQKDG LVGGMTFLQY IALGNANPVD FEQKRVTG V IFYLIFAIVT AILLLNLFIA MLADTYTRVS TQAMVEFRYR KAKLMASYSR RDFVCPPFNL LHLVCAAVGN GLRRLVWGP DGFTPVSMRK NETVPLFSWY FPQGEEMRQV VVLQRRVVDD FLNSNRVALF REKLNAELPN LVHEMLKQKG KGDGGALAGG GAAASTTVL ATAVSVTAAA GH

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Macromolecule #2: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Macromolecule #3: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #4: (2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bi...

MacromoleculeName: (2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate
type: ligand / ID: 4 / Number of copies: 4 / Formula: PIK
Molecular weightTheoretical: 970.992 Da
Chemical component information

ChemComp-PIK:
(2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate

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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

Concentration2 mg/mL
BufferpH: 8 / Details: 150 mM NaCl, 20 mM Tris-HCl pH 8.0, 1 mM BME
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 71.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 255973

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6pw5:
Cryo-EM Structure of Thermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas reinhardtii in Nanodiscs

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