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Yorodumi- EMDB-7972: cryo-EM reconstruction of the mitochondrial calcium uniporter (MC... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7972 | |||||||||
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Title | cryo-EM reconstruction of the mitochondrial calcium uniporter (MCU) from Zebrafish | |||||||||
Map data | Cryo-EM structure of the mitochondrial calcium uniporter | |||||||||
Sample |
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Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 Å | |||||||||
Authors | Long SB / Baradaran R / Wang C | |||||||||
Citation | Journal: Nature / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7972.map.gz | 58.8 MB | EMDB map data format | |
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Header (meta data) | emd-7972-v30.xml emd-7972.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_7972.png | 32.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7972 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7972 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7972.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the mitochondrial calcium uniporter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.384 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Mitochondrial Calcium Uniporter (MCU) from Zebrafish
Entire | Name: Mitochondrial Calcium Uniporter (MCU) from Zebrafish |
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Components |
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-Supramolecule #1: Mitochondrial Calcium Uniporter (MCU) from Zebrafish
Supramolecule | Name: Mitochondrial Calcium Uniporter (MCU) from Zebrafish / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 133 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI - |
-Macromolecule #1: Mitochondrial Calcium Uniporter (MCU) from Zebrafish
Macromolecule | Name: Mitochondrial Calcium Uniporter (MCU) from Zebrafish / type: protein_or_peptide / ID: 1 Details: Zebrafish (Danio rerio) MCU expressed in mammalian cells and purified in digitonin detergent. Enantiomer: LEVO |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LLCSPAAEDV SVVYQNGLPV ISVRLPSRRE R CQFTLKPL SDTVGVFLQQ LQAEDRGIDR VTIYSADGAR IASSTGIDIL LMDNFKLVIN DT SYLVQPP RRDLLPHEDG ERLNDVKILV QQLYTTLRIE EHQLNKEREL IGRLEDLNSQ LQP LEKVKE ELSKKAERRT ...String: LLCSPAAEDV SVVYQNGLPV ISVRLPSRRE R CQFTLKPL SDTVGVFLQQ LQAEDRGIDR VTIYSADGAR IASSTGIDIL LMDNFKLVIN DT SYLVQPP RRDLLPHEDG ERLNDVKILV QQLYTTLRIE EHQLNKEREL IGRLEDLNSQ LQP LEKVKE ELSKKAERRT TWVLWGGMAY MATQFGILAR LTWWEYSWDI MEPVTYFITY GTAM AMYAY FVLTRQEYLY PDARDRQYLL FFHRGAKRTR FDIEKYNKLK DAIAEAELDL KRLRD PLQL NLPIQQIDTS KD |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8.5 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 - 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-46 / Number grids imaged: 3 / Number real images: 3500 / Average exposure time: 0.13 sec. / Average electron dose: 2.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 269574 | ||||||||
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CTF correction | Software - Name: CTFFIND (ver. 4.1.5) | ||||||||
Startup model | Type of model: INSILICO MODEL / In silico model: Generated using Cryosparc | ||||||||
Initial angle assignment | Type: RANDOM ASSIGNMENT Software:
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Final 3D classification | Number classes: 1 / Avg.num./class: 196272 / Software - Name: FREALIGN (ver. cisTEM 1.0) / Software - details: cisTEM 1.0 | ||||||||
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN (ver. cisTEM 1.0) / Software - details: cisTEM 1.0 | ||||||||
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. cisTEM 1.0) / Software - details: cisTEM 1.0 / Number images used: 196272 |