+Open data
-Basic information
Entry | Database: PDB / ID: 6co7 | |||||||||
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Title | Structure of the nvTRPM2 channel in complex with Ca2+ | |||||||||
Components | Predicted protein | |||||||||
Keywords | MEMBRANE PROTEIN / Ion channel / TRPM2 / Ca2+ binding / Nematostella vectensis | |||||||||
Function / homology | Function and homology information ligand-gated sodium channel activity / ADP-ribose diphosphatase activity / ligand-gated calcium channel activity / sodium ion transmembrane transport / calcium ion transmembrane transport / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Nematostella vectensis (starlet sea anemone) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||
Authors | Zhang, Z. / Toth, B. / Szollosi, A. / Chen, J. / Csanady, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2018 Title: Structure of a TRPM2 channel in complex with Ca explains unique gating regulation. Authors: Zhe Zhang / Balázs Tóth / Andras Szollosi / Jue Chen / László Csanády / Abstract: Transient receptor potential melastatin 2 (TRPM2) is a Ca-permeable cation channel required for immune cell activation, insulin secretion, and body heat control. TRPM2 is activated by cytosolic Ca, ...Transient receptor potential melastatin 2 (TRPM2) is a Ca-permeable cation channel required for immune cell activation, insulin secretion, and body heat control. TRPM2 is activated by cytosolic Ca, phosphatidyl-inositol-4,5-bisphosphate and ADP ribose. Here, we present the ~3 Å resolution electron cryo-microscopic structure of TRPM2 from , 63% similar in sequence to human TRPM2, in the Ca-bound closed state. Compared to other TRPM channels, TRPM2 exhibits unique structural features that correlate with its function. The pore is larger and more negatively charged, consistent with its high Ca selectivity and larger conductance. The intracellular Ca binding sites are connected to the pore and cytosol, explaining the unusual dependence of TRPM2 activity on intra- and extracellular Ca. In addition, the absence of a post-filter motif is likely the cause of the rapid inactivation of human TRPM2. Together, our cryo-EM and electrophysiology studies provide a molecular understanding of the unique gating mechanism of TRPM2. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6co7.cif.gz | 900.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6co7.ent.gz | 721.8 KB | Display | PDB format |
PDBx/mmJSON format | 6co7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6co7_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 6co7_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6co7_validation.xml.gz | 116.6 KB | Display | |
Data in CIF | 6co7_validation.cif.gz | 167.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/6co7 ftp://data.pdbj.org/pub/pdb/validation_reports/co/6co7 | HTTPS FTP |
-Related structure data
Related structure data | 7542MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 176663.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nematostella vectensis (starlet sea anemone) Gene: v1g248535 / Production host: Homo sapiens (human) / References: UniProt: A7T1N0 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 67 molecules
#3: Chemical | ChemComp-CLR / #4: Chemical | ChemComp-POV / ( #5: Chemical | ChemComp-CA / #6: Chemical | |
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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 |
-Sample preparation
Component | Name: nvTRPM2 tetramer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Nematostella vectensis (starlet sea anemone) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated defocus min: 700 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.5 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: 1550 |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 196198 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104268 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |