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Open data
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Basic information
Entry | Database: PDB / ID: 6o20 | |||||||||||||||||||||||||||
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Title | Cryo-EM structure of TRPV5 with calmodulin bound | |||||||||||||||||||||||||||
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![]() | MEMBRANE PROTEIN / TRP channel | |||||||||||||||||||||||||||
Function / homology | ![]() regulation of urine volume / positive regulation of ryanodine-sensitive calcium-release channel activity / calcium ion import across plasma membrane / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / calcium ion transmembrane transport / calcium channel activity / spindle pole ...regulation of urine volume / positive regulation of ryanodine-sensitive calcium-release channel activity / calcium ion import across plasma membrane / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / calcium ion transmembrane transport / calcium channel activity / spindle pole / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / protein domain specific binding / calcium ion binding / protein-containing complex / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||||||||
![]() | Dang, S. / van Goor, M.K. / Asarnow, D. / Wang, Y. / Julius, D. / Cheng, Y. / van der Wijst, J. | |||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Structural insight into TRPV5 channel function and modulation. Authors: Shangyu Dang / Mark K van Goor / Daniel Asarnow / YongQiang Wang / David Julius / Yifan Cheng / Jenny van der Wijst / ![]() ![]() Abstract: TRPV5 (transient receptor potential vanilloid 5) is a unique calcium-selective TRP channel essential for calcium homeostasis. Unlike other TRPV channels, TRPV5 and its close homolog, TRPV6, do not ...TRPV5 (transient receptor potential vanilloid 5) is a unique calcium-selective TRP channel essential for calcium homeostasis. Unlike other TRPV channels, TRPV5 and its close homolog, TRPV6, do not exhibit thermosensitivity or ligand-dependent activation but are constitutively open at physiological membrane potentials and modulated by calmodulin (CaM) in a calcium-dependent manner. Here we report high-resolution electron cryomicroscopy structures of truncated and full-length TRPV5 in lipid nanodiscs, as well as of a TRPV5 W583A mutant and TRPV5 in complex with CaM. These structures highlight the mechanism of calcium regulation and reveal a flexible stoichiometry of CaM binding to TRPV5. | |||||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 469.9 KB | Display | ![]() |
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PDB format | ![]() | 379.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 70.7 KB | Display | |
Data in CIF | ![]() | 106.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0607MC ![]() 0593C ![]() 0594C ![]() 0605C ![]() 6o1nC ![]() 6o1pC ![]() 6o1uC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data #1: Automated picked particle stack of TRPV5 with calmodulin bound [picked particles - single frame - unprocessed]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 82899.656 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 19023.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() References: UniProt: P62157 #3: Chemical | ChemComp-CA / Compound details | THE AUTHORS STATE THAT CHAIN E IS THE C-TERMINAL END OF ONE SUBUNIT OF TRPV5, BUT THEY ARE NOT SURE WHICH ONE. | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Complex of TRPV5 with calmodulin bound / Type: CELL / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 63 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: 1135 |
Image scans | Movie frames/image: 50 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 482348 / Details: automated picked | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34604 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | |||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6O1N Accession code: 6O1N / Source name: PDB / Type: experimental model |