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- EMDB-7828: Cryo-EM structure of the mitochondrial calcium uniporter from N. ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7828 | ||||||||||||
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Title | Cryo-EM structure of the mitochondrial calcium uniporter from N. fischeri bound to saposin | ||||||||||||
![]() | Cryo-EM structure of MCU from N. fischeri low pass-filtered to 5.0 Angstrom resolution to show saposin molecules | ||||||||||||
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![]() | Mitochondria / calcium channel / TRANSPORT PROTEIN | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | ||||||||||||
![]() | Nguyen NX / Armache J-P | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
Images | ![]() | 553.2 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 37.2 MB 37.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d80MC ![]() 7826C ![]() 6d7wC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of MCU from N. fischeri low pass-filtered to 5.0 Angstrom resolution to show saposin molecules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution
File | emd_7828_additional.map | ||||||||||||
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Annotation | Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution
File | emd_7828_additional_1.map | ||||||||||||
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Annotation | Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mitochondrial calcium uniporter / saposin complex
Entire | Name: Mitochondrial calcium uniporter / saposin complex |
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Components |
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-Supramolecule #1: Mitochondrial calcium uniporter / saposin complex
Supramolecule | Name: Mitochondrial calcium uniporter / saposin complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #3: Mitochondrial calcium uniporter
Supramolecule | Name: Mitochondrial calcium uniporter / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: saposin
Supramolecule | Name: saposin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Saposin A
Macromolecule | Name: Saposin A / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.911511 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK) |
-Macromolecule #2: Mitochondrial calcium uniporter
Macromolecule | Name: Mitochondrial calcium uniporter / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.928004 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: An initial model was generated by RELION. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83343 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |