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Yorodumi- PDB-6wdn: Cryo-EM structure of mitochondrial calcium uniporter holocomplex ... -
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-Basic information
Entry | Database: PDB / ID: 6wdn | ||||||
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Title | Cryo-EM structure of mitochondrial calcium uniporter holocomplex in low Ca2+ | ||||||
Components |
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Keywords | MEMBRANE PROTEIN | ||||||
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 / Mitochondrial calcium ion transport / uniplex complex / 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 / Mitochondrial calcium ion transport / uniplex complex / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / channel activator activity / calcium ion sensor activity / calcium import into the mitochondrion / cellular response to calcium ion starvation / calcium ion import / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / calcium channel inhibitor activity / calcium channel complex / Mitochondrial protein degradation / cellular response to calcium ion / protein complex oligomerization / mitochondrial membrane / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / protein homooligomerization / mitochondrial intermembrane space / defense response / glucose homeostasis / protein-macromolecule adaptor activity / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / calcium ion binding / mitochondrion / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Feng, L. / Zhang, J. / Fan, M. | ||||||
Citation | Journal: Nature / Year: 2020 Title: Structure and mechanism of the mitochondrial Ca uniporter holocomplex. Authors: Minrui Fan / Jinru Zhang / Chen-Wei Tsai / Benjamin J Orlando / Madison Rodriguez / Yan Xu / Maofu Liao / Ming-Feng Tsai / Liang Feng / Abstract: Mitochondria take up Ca through the mitochondrial calcium uniporter complex to regulate energy production, cytosolic Ca signalling and cell death. In mammals, the uniporter complex (uniplex) contains ...Mitochondria take up Ca through the mitochondrial calcium uniporter complex to regulate energy production, cytosolic Ca signalling and cell death. In mammals, the uniporter complex (uniplex) contains four core components: the pore-forming MCU protein, the gatekeepers MICU1 and MICU2, and an auxiliary subunit, EMRE, essential for Ca transport. To prevent detrimental Ca overload, the activity of MCU must be tightly regulated by MICUs, which sense changes in cytosolic Ca concentrations to switch MCU on and off. Here we report cryo-electron microscopic structures of the human mitochondrial calcium uniporter holocomplex in inhibited and Ca-activated states. These structures define the architecture of this multicomponent Ca-uptake machinery and reveal the gating mechanism by which MICUs control uniporter activity. Our work provides a framework for understanding regulated Ca uptake in mitochondria, and could suggest ways of modulating uniporter activity to treat diseases related to mitochondrial Ca overload. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6wdn.cif.gz | 277.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wdn.ent.gz | 231.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wdn_validation.pdf.gz | 828.9 KB | Display | wwPDB validaton report |
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Full document | 6wdn_full_validation.pdf.gz | 860 KB | Display | |
Data in XML | 6wdn_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 6wdn_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/6wdn ftp://data.pdbj.org/pub/pdb/validation_reports/wd/6wdn | HTTPS FTP |
-Related structure data
Related structure data | 21642MC 6wdoC 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: 39755.582 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 | ||
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#2: Protein | Mass: 41900.891 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 | ||
#3: Protein | Mass: 5667.833 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMDT1, C22orf32, EMRE / Production host: Homo sapiens (human) / References: UniProt: Q9H4I9 #4: Protein | Mass: 21256.521 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Production host: Homo sapiens (human) / References: UniProt: Q8NE86 |
-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: Calcium uptake protein 2, mitochondrial, Calcium uptake protein 1, mitochondrial, Essential MCU regulator, mitochondrial, Calcium uniporter protein, mitochondrial complex Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 7.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE |
-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 / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 53 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53216 / Symmetry type: POINT |