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- EMDB-7803: Cryo-EM map of F.graminearum Mitochondrial Calcium Uniporter in P... -

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Basic information

Entry
Database: EMDB / ID: EMD-7803
TitleCryo-EM map of F.graminearum Mitochondrial Calcium Uniporter in PMAL-C8
Map dataCryo-EM map of FgMCU in PMAL-C8 filtered to 5A with -300 bfactor
Sample
  • Complex: FgMCU in amphipol PMAL-C8
Biological speciesFusarium graminearum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsOrlando BJ / Liao M
CitationJournal: Nature / Year: 2018
Title: X-ray and cryo-EM structures of the mitochondrial calcium uniporter.
Authors: Chao Fan / Minrui Fan / Benjamin J Orlando / Nathan M Fastman / Jinru Zhang / Yan Xu / Melissa G Chambers / Xiaofang Xu / Kay Perry / Maofu Liao / Liang Feng /
Abstract: Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the ...Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU). Here, we determined the structures of the pore-forming MCU proteins from two fungi by X-ray crystallography and single-particle cryo-electron microscopy. The stoichiometry, overall architecture, and individual subunit structure differed markedly from those described in the recent nuclear magnetic resonance structure of Caenorhabditis elegans MCU. We observed a dimer-of-dimer architecture across species and chemical environments, which was corroborated by biochemical experiments. Structural analyses and functional characterization uncovered the roles of key residues in the pore. These results reveal a new ion channel architecture, provide insights into calcium coordination, selectivity and conduction, and establish a structural framework for understanding the mechanism of mitochondrial calcium uniporter function.
History
DepositionApr 20, 2018-
Header (metadata) releaseMay 16, 2018-
Map releaseSep 19, 2018-
UpdateSep 19, 2018-
Current statusSep 19, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0221
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0221
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7803.png

Downloads & links

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Map

FileDownload / File: emd_7803.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of FgMCU in PMAL-C8 filtered to 5A with -300 bfactor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 220 pix.
= 215.6 Å		0.98 Å/pix.
x 220 pix.
= 215.6 Å		0.98 Å/pix.
x 220 pix.
= 215.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0221 / Movie #1: 0.0221
Minimum - Maximum-0.030231215 - 0.08037201
Average (Standard dev.)-0.000013509092 (±0.00454017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions220220220
Spacing220220220
CellA=B=C: 215.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z215.600215.600215.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS220220220
D min/max/mean-0.0300.080-0.000

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Supplemental data

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Additional map: unfiltered cryo-EM map of FgMCU in PMAL-C8

Fileemd_7803_additional.map
Annotationunfiltered cryo-EM map of FgMCU in PMAL-C8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FgMCU in amphipol PMAL-C8

EntireName: FgMCU in amphipol PMAL-C8
Components
  • Complex: FgMCU in amphipol PMAL-C8

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Supramolecule #1: FgMCU in amphipol PMAL-C8

SupramoleculeName: FgMCU in amphipol PMAL-C8 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Fusarium graminearum (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
10.0 mMC4H11NO3tris
2.0 mMCaCl2calcium chloride
0.3 mMC13H17F13NO4Pfluorinated fos-choline 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 115063
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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