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Yorodumi- EMDB-7826: Cryo-EM structure of the mitochondrial calcium uniporter from N. ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7826 | ||||||||||||
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Title | Cryo-EM structure of the mitochondrial calcium uniporter from N. fischeri at 3.8 Angstrom resolution | ||||||||||||
Map data | Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution | ||||||||||||
Sample |
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Keywords | Mitochondria / calcium channel / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information uniporter activity / uniplex complex / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium channel activity / protein homotetramerization / mitochondrial inner membrane Similarity search - Function | ||||||||||||
Biological species | Aspergillus fischeri (mold) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Nguyen NX / Armache J-P | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM structure of a fungal mitochondrial calcium uniporter. Authors: Nam X Nguyen / Jean-Paul Armache / Changkeun Lee / Yi Yang / Weizhong Zeng / Vamsi K Mootha / Yifan Cheng / Xiao-Chen Bai / Youxing Jiang / Abstract: The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel localized to the inner mitochondrial membrane. Here, we describe the structure of an MCU orthologue from the fungus ...The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel localized to the inner mitochondrial membrane. Here, we describe the structure of an MCU orthologue from the fungus Neosartorya fischeri (NfMCU) determined to 3.8 Å resolution by phase-plate cryo-electron microscopy. The channel is a homotetramer with two-fold symmetry in its amino-terminal domain (NTD) that adopts a similar structure to that of human MCU. The NTD assembles as a dimer of dimers to form a tetrameric ring that connects to the transmembrane domain through an elongated coiled-coil domain. The ion-conducting pore domain maintains four-fold symmetry, with the selectivity filter positioned at the start of the pore-forming TM2 helix. The aspartate and glutamate sidechains of the conserved DIME motif are oriented towards the central axis and separated by one helical turn. The structure of NfMCU offers insights into channel assembly, selective calcium permeation, and inhibitor binding. | ||||||||||||
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_7826.map.gz | 37.2 MB | EMDB map data format | |
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Header (meta data) | emd-7826-v30.xml emd-7826.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_7826.png | 63 KB | ||
Filedesc metadata | emd-7826.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7826 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7826 | HTTPS FTP |
-Validation report
Summary document | emd_7826_validation.pdf.gz | 548.4 KB | Display | EMDB validaton report |
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Full document | emd_7826_full_validation.pdf.gz | 548 KB | Display | |
Data in XML | emd_7826_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_7826_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7826 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7826 | HTTPS FTP |
-Related structure data
Related structure data | 6d7wMC 7828C 6d80C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7826.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 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
Entire | Name: Mitochondrial calcium uniporter |
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Components |
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-Supramolecule #1: Mitochondrial calcium uniporter
Supramolecule | Name: Mitochondrial calcium uniporter / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Aspergillus fischeri (mold) |
-Macromolecule #1: Mitochondrial calcium uniporter
Macromolecule | Name: Mitochondrial calcium uniporter / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Aspergillus fischeri (mold) |
Molecular weight | Theoretical: 47.928004 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GSDKRGPQSA EPDPLERLEV KKVQQQHENE KDDSGRDTKS GGKVAKAMTK GDTIAGKLLT TPSRLFKLLI PLTTINRKDI EQIAILIHP QQPLSHLERL IQSEVPPIED ENGQKRPPFV SFIALQLEQD AIRPKRGMYE GTDAEIHRVE GGKDDATVAK R GEDFQEVD ...String: GSDKRGPQSA EPDPLERLEV KKVQQQHENE KDDSGRDTKS GGKVAKAMTK GDTIAGKLLT TPSRLFKLLI PLTTINRKDI EQIAILIHP QQPLSHLERL IQSEVPPIED ENGQKRPPFV SFIALQLEQD AIRPKRGMYE GTDAEIHRVE GGKDDATVAK R GEDFQEVD ETFSYLRRPG PGQGDKEQRF IRWSQSTEIG DFIRDAARAK EFIVTIEGAP AGLEQIHVAV PSFDERTYFL RM RLRKISR RIQGLAEIKH ECDALAHRGA QRVALGGFGI LAFWWYIVYK LTFETDLGWD TMEPVTYLVS LSTLMGGYLW FLY HNREIS YRSALDFTIN ARQKKLYQMK GIDLQVWESL IDEANAIRRE IKNIAAEYDV DWDERKDEQD DRVTEALKKE RRLK NGSQK EERPKDDRDD D UniProtKB: Calcium uniporter protein, mitochondrial |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM HEPES, pH 7.5, 300 mM sodium chloride, 1 mM calcium chloride, 2% glycerol |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | N. fischeri MCU was reconstituted into lipid using E. coli total lipids and human saposin A as the membrane scaffolding protein. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: An initial model was generated by RELION. |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83343 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |