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- EMDB-7828: Cryo-EM structure of the mitochondrial calcium uniporter from N. ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7828
TitleCryo-EM structure of the mitochondrial calcium uniporter from N. fischeri bound to saposin
Map dataCryo-EM structure of MCU from N. fischeri low pass-filtered to 5.0 Angstrom resolution to show saposin molecules
Sample
  • Organelle or cellular component: Mitochondrial calcium uniporter / saposin complex
    • Organelle or cellular component: Mitochondrial calcium uniporter
      • Protein or peptide: Mitochondrial calcium uniporter
    • Complex: saposin
      • Protein or peptide: Saposin A
  • Ligand: CALCIUM ION
KeywordsMitochondria / calcium channel / TRANSPORT PROTEIN
Function / homologyuniporter activity / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / uniplex complex / calcium import into the mitochondrion / mitochondrial calcium ion homeostasis / calcium channel activity / Calcium uniporter protein
Function and homology information
Biological speciesAspergillus fischeri (mold) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsNguyen NX / Armache J-P
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
CitationJournal: 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
DepositionApr 25, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseJul 11, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6d80
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7828.png

Downloads & links

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Map

FileDownload / File: emd_7828.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of MCU from N. fischeri low pass-filtered to 5.0 Angstrom resolution to show saposin molecules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 220 pix.
= 184.8 Å		0.84 Å/pix.
x 220 pix.
= 184.8 Å		0.84 Å/pix.
x 220 pix.
= 184.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.006093651 - 0.021429818
Average (Standard dev.)0.0003616772 (±0.0017737029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 184.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z184.800184.800184.800
α/β/γ90.00090.00090.000
start NX/NY/NZ887264
NX/NY/NZ104112143
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0060.0210.000

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Supplemental data

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Additional map: Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution

Fileemd_7828_additional.map
AnnotationCryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution

Fileemd_7828_additional_1.map
AnnotationCryo-EM structure of MCU from N. fischeri at 3.8 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial calcium uniporter / saposin complex

EntireName: Mitochondrial calcium uniporter / saposin complex
Components
  • Organelle or cellular component: Mitochondrial calcium uniporter / saposin complex
    • Organelle or cellular component: Mitochondrial calcium uniporter
      • Protein or peptide: Mitochondrial calcium uniporter
    • Complex: saposin
      • Protein or peptide: Saposin A
  • Ligand: CALCIUM ION

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Supramolecule #1: Mitochondrial calcium uniporter / saposin complex

SupramoleculeName: 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

SupramoleculeName: Mitochondrial calcium uniporter / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Aspergillus fischeri (mold)

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Supramolecule #2: saposin

SupramoleculeName: saposin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Saposin A

MacromoleculeName: Saposin A / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.911511 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: (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)

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Macromolecule #2: Mitochondrial calcium uniporter

MacromoleculeName: Mitochondrial calcium uniporter / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aspergillus fischeri (mold)
Molecular weightTheoretical: 47.928004 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES, pH 7.5, 300 mM sodium chloride, 1 mM calcium chloride, 2% glycerol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsN. 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

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: An initial model was generated by RELION.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83343
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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