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Yorodumi- PDB-6pkv: Cryo-EM structure of the zebrafish TRPM2 channel in the apo confo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pkv | ||||||
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Title | Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with C4 symmetry | ||||||
Components | Transient receptor potential cation channel subfamily M member 2 | ||||||
Keywords | TRANSPORT PROTEIN / warmth sensor / redox sensor / calcium-permeable ion channel / TRP channel / TRPM channel / ion channel / ADP-ribose | ||||||
Function / homology | Function and homology information TRP channels / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / ligand-gated monoatomic cation channel activity / release of sequestered calcium ion into cytosol / monoatomic ion channel activity / calcium ion transmembrane transport / calcium channel activity ...TRP channels / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / ligand-gated monoatomic cation channel activity / release of sequestered calcium ion into cytosol / monoatomic ion channel activity / calcium ion transmembrane transport / calcium channel activity / protein homotetramerization / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Yin, Y. / Wu, M. / Hsu, A.L. / Borschel, W.F. / Borgnia, M.J. / Lander, G.C. / Lee, S.-Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel. Authors: Ying Yin / Mengyu Wu / Allen L Hsu / William F Borschel / Mario J Borgnia / Gabriel C Lander / Seok-Yong Lee / Abstract: The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca. The ...The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca. The recently published TRPM2 structures from Danio rerio in the ligand-free and the ADPR/Ca-bound conditions represent the channel in closed and open states, which uncovered substantial tertiary and quaternary conformational rearrangements. However, it is unclear how these rearrangements are achieved within the tetrameric channel during channel gating. Here we report the cryo-electron microscopy structures of Danio rerio TRPM2 in the absence of ligands, in complex with Ca alone, and with both ADPR and Ca, resolved to ~4.3 Å, ~3.8 Å, and ~4.2 Å, respectively. In contrast to the published results, our studies capture ligand-bound TRPM2 structures in two-fold symmetric intermediate states, offering a glimpse of the structural transitions that bridge the closed and open conformations. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pkv.cif.gz | 712.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pkv.ent.gz | 530.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pkv_validation.pdf.gz | 987.5 KB | Display | wwPDB validaton report |
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Full document | 6pkv_full_validation.pdf.gz | 1002.7 KB | Display | |
Data in XML | 6pkv_validation.xml.gz | 94.8 KB | Display | |
Data in CIF | 6pkv_validation.cif.gz | 153.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/6pkv ftp://data.pdbj.org/pub/pdb/validation_reports/pk/6pkv | HTTPS FTP |
-Related structure data
Related structure data | 20367MC 7822C 6d73C 6pkwC 6pkxC 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
#1: Protein | Mass: 167608.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trpm2 / Production host: Homo sapiens (human) / References: UniProt: A0A0R4IMY7*PLUS |
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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: Transient receptor potential cation channel subfamily M member 2 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 3.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298.15 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 / Nominal magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.6 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3776 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 301199 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58005 Details: No symmetry (C1) was imposed during reconstructions and classifications. C4 symmetry was imposed during the final 3D auto-refinement. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 150 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6D73 Pdb chain-ID: A / Accession code: 6D73 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||
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