+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6455 | |||||||||
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Title | TRPV2 ion channel from rabbit | |||||||||
Map data | TRPV2, sharpened with a B factor of -76 using RELION postprocess | |||||||||
Sample |
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Keywords | TRP channel / ion transport | |||||||||
Function / homology | Function and homology information growth cone membrane / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone / calcium channel activity / positive regulation of cold-induced thermogenesis / cell body / cell surface / identical protein binding Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Herzik MA / Zubcevic L / Chung BC / Lander GC / Lee SY | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: Cryo-electron microscopy structure of the TRPV2 ion channel. Authors: Lejla Zubcevic / Mark A Herzik / Ben C Chung / Zhirui Liu / Gabriel C Lander / Seok-Yong Lee / Abstract: Transient receptor potential vanilloid (TRPV) cation channels are polymodal sensors involved in a variety of physiological processes. TRPV2, a member of the TRPV family, is regulated by temperature, ...Transient receptor potential vanilloid (TRPV) cation channels are polymodal sensors involved in a variety of physiological processes. TRPV2, a member of the TRPV family, is regulated by temperature, by ligands, such as probenecid and cannabinoids, and by lipids. TRPV2 has been implicated in many biological functions, including somatosensation, osmosensation and innate immunity. Here we present the atomic model of rabbit TRPV2 in its putative desensitized state, as determined by cryo-EM at a nominal resolution of ∼4 Å. In the TRPV2 structure, the transmembrane segment 6 (S6), which is involved in gate opening, adopts a conformation different from the one observed in TRPV1. Structural comparisons of TRPV1 and TRPV2 indicate that a rotation of the ankyrin-repeat domain is coupled to pore opening via the TRP domain, and this pore opening can be modulated by rearrangements in the secondary structure of S6. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6455.map.gz | 14.5 MB | EMDB map data format | |
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Header (meta data) | emd-6455-v30.xml emd-6455.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6455_fsc.xml | 9 KB | Display | FSC data file |
Images | 400_6455.gif 80_6455.gif | 59.5 KB 4.2 KB | ||
Others | emd_6455_additional_1.map.gz emd_6455_half_map_1.map.gz emd_6455_half_map_2.map.gz | 45.9 MB 45.9 MB 45.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6455 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6455 | HTTPS FTP |
-Validation report
Summary document | emd_6455_validation.pdf.gz | 342.6 KB | Display | EMDB validaton report |
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Full document | emd_6455_full_validation.pdf.gz | 341.7 KB | Display | |
Data in XML | emd_6455_validation.xml.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6455 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6455 | HTTPS FTP |
-Related structure data
Related structure data | 5an8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6455.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TRPV2, sharpened with a B factor of -76 using RELION postprocess | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 6455 additional 1.map
File | emd_6455_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6455 half map 1.map
File | emd_6455_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6455 half map 2.map
File | emd_6455_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rabbit TRPV2
Entire | Name: Rabbit TRPV2 |
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Components |
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-Supramolecule #1000: Rabbit TRPV2
Supramolecule | Name: Rabbit TRPV2 / type: sample / ID: 1000 / Oligomeric state: homotetramer / Number unique components: 1 |
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-Macromolecule #1: TRPV2
Macromolecule | Name: TRPV2 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 / Recombinant plasmid: pFastBac |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.6 / Details: PBS |
Grid | Details: 400 mesh C-flat copper grid with carbon support, 1.2 micron holes spaced 1.3 microns |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 2.5 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77 K / Max: 79 K / Average: 78 K |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism was corrected at 22500 times magnification using Thon rings visualized with a K2 camera. |
Details | Data was acquired using Leginon and collected in K2 super-resolution mode. |
Date | May 12, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 747 / Average electron dose: 57 e/Å2 / Details: 50 frames, 200 ms per frame |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |