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- EMDB-7800: Cryo-EM map of F.graminearum Mitochondrial Calcium Uniporter in l... -

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Basic information

Entry
Database: EMDB / ID: EMD-7800
TitleCryo-EM map of F.graminearum Mitochondrial Calcium Uniporter in lipid nanodisc - overall
Map dataCryoEM map of FgMCU in nanodisc filtered to 4.9A with -300 bfactor
Sample
  • Complex: Fusarium graminearum Mitochondrial Calcium Uniporter in lipid nanodiscs - overall
Biological speciesFusarium graminearum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 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: 0.0242
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7800.png

Downloads & links

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Map

FileDownload / File: emd_7800.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of FgMCU in nanodisc filtered to 4.9A with -300 bfactor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 192 pix.
= 224.448 Å		1.17 Å/pix.
x 192 pix.
= 224.448 Å		1.17 Å/pix.
x 192 pix.
= 224.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.169 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242 / Movie #1: 0.0242
Minimum - Maximum-0.041915152 - 0.09261778
Average (Standard dev.)0.000060519193 (±0.005770619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-82-82-82
Dimensions192192192
Spacing192192192
CellA=B=C: 224.448 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1691.1691.169
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z224.448224.448224.448
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-82-82-82
NC/NR/NS192192192
D min/max/mean-0.0420.0930.000

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Supplemental data

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Additional map: Unfiltered cryoEM map of FgMCU in nanodisc

Fileemd_7800_additional.map
AnnotationUnfiltered cryoEM map of FgMCU in nanodisc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fusarium graminearum Mitochondrial Calcium Uniporter in lipid nan...

EntireName: Fusarium graminearum Mitochondrial Calcium Uniporter in lipid nanodiscs - overall
Components
  • Complex: Fusarium graminearum Mitochondrial Calcium Uniporter in lipid nanodiscs - overall

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Supramolecule #1: Fusarium graminearum Mitochondrial Calcium Uniporter in lipid nan...

SupramoleculeName: Fusarium graminearum Mitochondrial Calcium Uniporter in lipid nanodiscs - overall
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 mMCaClcalcium chloride
0.3 mMFC-8fluorinated fos-choline 8
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Details: 15mA in Pelco EasyGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 92 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / 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: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 236959
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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