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- EMDB-7971: cryo-EM structure of the mitochondrial calcium uniporter MCU from... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7971 | |||||||||
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Title | cryo-EM structure of the mitochondrial calcium uniporter MCU from the fungus Cyphellophora europaea | |||||||||
![]() | Cryo-EM structure of the mitochondrial calcium uniporter | |||||||||
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![]() | mitochondria / calcium / ion channel / eukaryotic / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() uniporter activity / mitochondrial calcium ion homeostasis / calcium channel activity / mitochondrial inner membrane / membrane => GO:0016020 / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Long SB / Baradaran R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters. Authors: Rozbeh Baradaran / Chongyuan Wang / Andrew Francis Siliciano / Stephen Barstow Long / ![]() Abstract: The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel and a major route of calcium entry into mitochondria. How the channel catalyses ion permeation and achieves ...The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel and a major route of calcium entry into mitochondria. How the channel catalyses ion permeation and achieves ion selectivity are not well understood, partly because MCU is thought to have a distinct architecture in comparison to other cellular channels. Here we report cryo-electron microscopy reconstructions of MCU channels from zebrafish and Cyphellophora europaea at 8.5 Å and 3.2 Å resolutions, respectively. In contrast to a previous report of pentameric stoichiometry for MCU, both channels are tetramers. The atomic model of C. europaea MCU shows that a conserved WDXXEP signature sequence forms the selectivity filter, in which calcium ions are arranged in single file. Coiled-coil legs connect the pore to N-terminal domains in the mitochondrial matrix. In C. europaea MCU, the N-terminal domains assemble as a dimer of dimers; in zebrafish MCU, they form an asymmetric crescent. The structures define principles that underlie ion permeation and calcium selectivity in this unusual channel. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 200.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 115.1 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 594.9 KB | Display | ![]() |
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Full document | ![]() | 594.5 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dnfMC ![]() 7972C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the mitochondrial calcium uniporter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.861 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellopho...
Entire | Name: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea. |
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Components |
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-Supramolecule #1: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellopho...
Supramolecule | Name: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea. type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 158.328 KDa |
-Macromolecule #1: Mitochondrial calcium uniporter MCU
Macromolecule | Name: Mitochondrial calcium uniporter MCU / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.637176 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MTKGKLLTTP SRLLKLVLPL STVDHNTDRK DVAPLALLVH PQQPLSYLER LIQAELPPPD PQDSKSTTRS VTFRAMEAKD DEIKPRKKA DTEGGGGSDG SVQSYSGAGR EGEGKDEGEF VRWSPSTEIG DFIRDAARAK EFEVEIEGSP GVIKVAVPSF N DRTYYLRQ ...String: MTKGKLLTTP SRLLKLVLPL STVDHNTDRK DVAPLALLVH PQQPLSYLER LIQAELPPPD PQDSKSTTRS VTFRAMEAKD DEIKPRKKA DTEGGGGSDG SVQSYSGAGR EGEGKDEGEF VRWSPSTEIG DFIRDAARAK EFEVEIEGSP GVIKVAVPSF N DRTYYLRQ RLRRTSRKIS KLAAIKEECD KAAHRGAQRI ALAGCGGLIG YWYIVYRLTF ETDLGWDVME PVTYLVGLST LI GGYMWFL WHNREVSYRS ALNITVSARQ NKLYQAKGFS LQDWEGYLEE ANAMRREIKA VASEYDVDWN ETQDEGGDEK VTK ALRDER KNNNGTKNKS KEGEEDDEDD GEGEEF UniProtKB: Calcium uniporter protein |
-Macromolecule #2: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]...
Macromolecule | Name: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL type: ligand / ID: 2 / Number of copies: 8 / Formula: DGG |
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Molecular weight | Theoretical: 734.981 Da |
Chemical component information | ![]() ChemComp-DGG: |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot, blot force of 0. | ||||||||||||||||||
Details | Monodisperse sample |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 3 / Number real images: 6040 / Average exposure time: 0.2 sec. / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 136.58 / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-6dnf: |