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- EMDB-43542: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open co... -
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Open data
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Basic information
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Title | ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation | ||||||||||||
![]() | ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation | ||||||||||||
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![]() | ELIC / ![]() ![]() | ||||||||||||
Function / homology | ![]() extracellular ligand-gated monoatomic ion channel activity / ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Petroff II JT / Deng Z / Rau MJ / Fitzpatrick JAJ / Yuan P / Cheng WWL | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Authors: John T Petroff / Noah M Dietzen / Ezry Santiago-McRae / Brett Deng / Maya S Washington / Lawrence J Chen / K Trent Moreland / Zengqin Deng / Michael Rau / James A J Fitzpatrick / Peng Yuan / ...Authors: John T Petroff / Noah M Dietzen / Ezry Santiago-McRae / Brett Deng / Maya S Washington / Lawrence J Chen / K Trent Moreland / Zengqin Deng / Michael Rau / James A J Fitzpatrick / Peng Yuan / Thomas T Joseph / Jérôme Hénin / Grace Brannigan / Wayland W L Cheng / ![]() ![]() Abstract: Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. ...Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.5 KB 21.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.5 KB | Display | ![]() |
Images | ![]() | 34.1 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 16.9 MB 16.9 MB 16.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vuwMC ![]() 8d63C ![]() 8d64C ![]() 8d65C ![]() 8d66C ![]() 8d67C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.081 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in...
File | emd_43542_additional_1.map | ||||||||||||
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Annotation | ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in...
File | emd_43542_half_map_1.map | ||||||||||||
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Annotation | ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in...
File | emd_43542_half_map_2.map | ||||||||||||
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Annotation | ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 PO...
Entire | Name: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc |
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Components |
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-Supramolecule #1: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 PO...
Supramolecule | Name: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Erwinia chrysanthemi ligand-gated ion channel
Macromolecule | Name: Erwinia chrysanthemi ligand-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.011055 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: APADNAADAR PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGN KRLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE W WIRGKAST ...String: APADNAADAR PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGN KRLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE W WIRGKAST HISDIRYDHL SSVQPNQNEF SRITVRIDAV RNPSYYLWSF ILPLGLIIAA SWSVFWLESF SERLQTSFTL ML TVVAYAF YTSNILGRLP YTTYIDQMII AGYGSIFAAI LLIIFAHHRQ ANGVEDDLLI QRSRLAFPLG FLAIGCVLVI RFF TL UniProtKB: Cys-loop ligand-gated ion channel |
-Macromolecule #2: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...
Macromolecule | Name: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate type: ligand / ID: 2 / Number of copies: 5 / Formula: PGW |
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Molecular weight | Theoretical: 749.007 Da |
-Macromolecule #3: 2-AMINO-ETHANETHIOL
Macromolecule | Name: 2-AMINO-ETHANETHIOL / type: ligand / ID: 3 / Number of copies: 5 / Formula: DHL |
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Molecular weight | Theoretical: 77.149 Da |
Chemical component information | ![]() ChemComp-DHL: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.332 kPa / Details: H2 27.5 sccm O2 6.4 sccm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2 seconds before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 150.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Spherical aberration corrector: Microscope was equipped with a Cs corrector. Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 82.0 K / Max: 84.0 K |
Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 8 / Number real images: 1 / Average exposure time: 1.65 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |