+Open data
-Basic information
Entry | Database: PDB / ID: 6dt0 | ||||||
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Title | Cryo-EM structure of a mitochondrial calcium uniporter | ||||||
Components | Mitochondrial calcium uniporter | ||||||
Keywords | TRANSPORT PROTEIN / mitochondrial calcium uniporter / calcium-selective ion channel / calcium uptake / uniporter | ||||||
Function / homology | Function and homology information : / uniporter activity / uniplex complex / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium channel activity / identical protein binding Similarity search - Function | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Yoo, J. / Wu, M. / Yin, Y. / Herzik, M.A.J. / Lander, G.C. / Lee, S.-Y. | ||||||
Citation | Journal: Science / Year: 2018 Title: Cryo-EM structure of a mitochondrial calcium uniporter. Authors: Jiho Yoo / Mengyu Wu / Ying Yin / Mark A Herzik / Gabriel C Lander / Seok-Yong Lee / Abstract: Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary ...Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary mediator for calcium uptake into the mitochondrial matrix. Here, we present the cryo-electron microscopy structure of the full-length MCU from to an overall resolution of ~3.7 angstroms. Our structure reveals a tetrameric architecture, with the soluble and transmembrane domains adopting different symmetric arrangements within the channel. The conserved W-D-Φ-Φ-E-P-V-T-Y sequence motif of MCU pore forms a selectivity filter comprising two acidic rings separated by one helical turn along the central axis of the channel pore. The structure combined with mutagenesis gives insight into the basis of calcium recognition. | ||||||
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 | 6dt0.cif.gz | 309.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dt0.ent.gz | 244.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dt0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6dt0_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6dt0_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 6dt0_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/6dt0 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/6dt0 | HTTPS FTP |
-Related structure data
Related structure data | 8911MC 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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1 |
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-Components
#1: Protein | Mass: 52948.117 Da / Num. of mol.: 4 / Fragment: UNP residues 46-493 / Mutation: Y232A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: NCU08166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7S4I4 #2: Chemical | ChemComp-CA / | |
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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: Mitochondrial Calcium Uniporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Neurospora crassa (fungus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Final reconstruction comprises ~80% of MCU in nanodisc (crosslinked using BS3) and ~20% MCU in amphipol. |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 4 second blot time |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 65 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3686168 Details: 1,791,114 particles of MCU in amphipol, 1,895,054 particles of crosslinked MCU in nanodisc | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36537 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 100 |