+Open data
-Basic information
Entry | Database: PDB / ID: 6xjv | ||||||
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Title | MCU holocomplex in High-calcium state | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / ion channel | ||||||
Function / homology | Function and homology information 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 / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis ...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 / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity / calcium ion import / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / Mitochondrial protein degradation / calcium channel complex / mitochondrial membrane / calcium-mediated signaling / calcium channel activity / protein homooligomerization / positive regulation of insulin secretion / mitochondrial intermembrane space / defense response / protein complex oligomerization / glucose homeostasis / 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: 4.17 Å | ||||||
Authors | Wang, Y. / Jiang, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Structural insights into the Ca-dependent gating of the human mitochondrial calcium uniporter. Authors: Yan Wang / Yan Han / Ji She / Nam X Nguyen / Vamsi K Mootha / Xiao-Chen Bai / Youxing Jiang / Abstract: Mitochondrial Ca uptake is mediated by an inner mitochondrial membrane protein called the mitochondrial calcium uniporter. In humans, the uniporter functions as a holocomplex consisting of MCU, EMRE, ...Mitochondrial Ca uptake is mediated by an inner mitochondrial membrane protein called the mitochondrial calcium uniporter. In humans, the uniporter functions as a holocomplex consisting of MCU, EMRE, MICU1 and MICU2, among which MCU and EMRE form a subcomplex and function as the conductive channel while MICU1 and MICU2 are EF-hand proteins that regulate the channel activity in a Ca-dependent manner. Here, we present the EM structures of the human mitochondrial calcium uniporter holocomplex (uniplex) in the presence and absence of Ca, revealing distinct Ca dependent assembly of the uniplex. Our structural observations suggest that Ca changes the dimerization interaction between MICU1 and MICU2, which in turn determines how the MICU1-MICU2 subcomplex interacts with the MCU-EMRE channel and, consequently, changes the distribution of the uniplex assemblies between the blocked and unblocked states. | ||||||
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 | 6xjv.cif.gz | 702.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xjv.ent.gz | 571.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xjv_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6xjv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6xjv_validation.xml.gz | 90.9 KB | Display | |
Data in CIF | 6xjv_validation.cif.gz | 140.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/6xjv ftp://data.pdbj.org/pub/pdb/validation_reports/xj/6xjv | HTTPS FTP |
-Related structure data
Related structure data | 22215MC 6xjxC 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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-Components
#1: Protein | Mass: 39920.828 Da / Num. of mol.: 8 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 #2: Protein | Mass: 11454.140 Da / Num. of mol.: 8 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 #3: Protein | Mass: 54432.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1, CALC, CBARA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BPX6 #4: Protein | Mass: 49742.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IYU8 |
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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: MCU/EMRE/MICU1/MICU2 complex / Type: COMPLEX / Details: high calcium state / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.529 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was reconstituted in Msp1 nanodiscs |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: blot for 4 seconds before plunging |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2 sec. / Electron dose: 30.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING ONLY |
3D reconstruction | Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19924 / Symmetry type: POINT |