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Yorodumi- PDB-6xqn: Structure of a mitochondrial calcium uniporter holocomplex (MICU1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xqn | |||||||||
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Title | Structure of a mitochondrial calcium uniporter holocomplex (MICU1, MICU2, MCU, EMRE) in low Ca2+ | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN/CALCIUM BINDING PROTEIN / ion channel / calcium channel / mitochondrial calcium uniporter / MCU / EMRE / mitochondria / TRANSPORT PROTEIN-CALCIUM BINDING PROTEIN complex | |||||||||
Function / homology | Function and homology information mitochondrial crista junction / positive regulation of cristae formation / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration ...mitochondrial crista junction / positive regulation of cristae formation / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity / calcium import into the mitochondrion / cellular response to calcium ion starvation / calcium ion import / calcium channel inhibitor activity / calcium channel complex / Mitochondrial protein degradation / cellular response to calcium ion / mitochondrial membrane / calcium channel activity / protein homooligomerization / mitochondrial intermembrane space / defense response / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Tribolium castaneum (red flour beetle) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Long, S.B. / Wang, C. / Baradaran, R. / Jacewicz, A. / Delgado, B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: Structures reveal gatekeeping of the mitochondrial Ca uniporter by MICU1-MICU2. Authors: Chongyuan Wang / Agata Jacewicz / Bryce D Delgado / Rozbeh Baradaran / Stephen Barstow Long / Abstract: The mitochondrial calcium uniporter is a Ca-gated ion channel complex that controls mitochondrial Ca entry and regulates cell metabolism. MCU and EMRE form the channel while Ca-dependent regulation ...The mitochondrial calcium uniporter is a Ca-gated ion channel complex that controls mitochondrial Ca entry and regulates cell metabolism. MCU and EMRE form the channel while Ca-dependent regulation is conferred by MICU1 and MICU2 through an enigmatic process. We present a cryo-EM structure of an MCU-EMRE-MICU1-MICU2 holocomplex comprising MCU and EMRE subunits from the beetle Tribolium castaneum in complex with a human MICU1-MICU2 heterodimer at 3.3 Å resolution. With analogy to how neuronal channels are blocked by protein toxins, a uniporter interaction domain on MICU1 binds to a channel receptor site comprising MCU and EMRE subunits to inhibit ion flow under resting Ca conditions. A Ca-bound structure of MICU1-MICU2 at 3.1 Å resolution indicates how Ca-dependent changes enable dynamic response to cytosolic Ca signals. | |||||||||
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 | 6xqn.cif.gz | 237.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xqn.ent.gz | 178 KB | Display | PDB format |
PDBx/mmJSON format | 6xqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xqn_validation.pdf.gz | 859.7 KB | Display | wwPDB validaton report |
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Full document | 6xqn_full_validation.pdf.gz | 869.2 KB | Display | |
Data in XML | 6xqn_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 6xqn_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/6xqn ftp://data.pdbj.org/pub/pdb/validation_reports/xq/6xqn | HTTPS FTP |
-Related structure data
Related structure data | 22290MC 6xqoC 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: 7372.190 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC012057 / Production host: Homo sapiens (human) / References: UniProt: D6X268 #2: Protein | Mass: 23634.100 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC013837 / Production host: Homo sapiens (human) / References: UniProt: D6WIX5 #3: Protein | | Mass: 45422.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1, CALC, CBARA1 / Production host: Homo sapiens (human) / References: UniProt: Q9BPX6 #4: Protein | | Mass: 44980.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Production host: Homo sapiens (human) / References: UniProt: Q8IYU8 #5: Chemical | ChemComp-CA / | Has ligand of interest | N | |
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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
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse sample | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: 2 second blot, blot force of 0 |
-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: -3000 nm / Nominal defocus min: -1000 nm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 71 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 5 / Num. of real images: 21115 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 17440131 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350160 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 124 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient |