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- EMDB-8911: Cryo-EM structure of a mitochondrial calcium uniporter -

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Basic information

Entry
Database: EMDB / ID: 8911
TitleCryo-EM structure of a mitochondrial calcium uniporter
Map dataSingle-particle cryo-EM reconstruction of the N. crassa mitochondrial calcium uniporter
SampleMitochondrial Calcium Uniporter:
Mitochondrial calcium uniporter / ligand
Function / homologyCalcium uniporter protein, C-terminal / Mitochondrial calcium uniporter / mitochondrial calcium ion homeostasis / uniplex complex / calcium import into the mitochondrion / uniporter activity / integral component of mitochondrial inner membrane / calcium channel activity / Uncharacterized protein
Function and homology information
SourceNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsYoo J / Wu M / Yin Y / Herzik MAJ / Lander GC / Lee S-Y
CitationJournal: Science / Year: 2018
Title: Cryo-EM structure of a mitochondrial calcium uniporter.
Authors: Jiho Yoo / Mengyu Wu / Ying Yin / Mark A Herzik / Gabriel C Lander / Seok-Yong Lee
Abstract: Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary ...Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary mediator for calcium uptake into the mitochondrial matrix. Here we present the cryo-electron microscopy structure of the full-length MCU from to an overall resolution of ~3.7 Å. Our structure reveals a tetrameric architecture, with the soluble and transmembrane domains adopting different symmetric arrangements within the channel. The conserved W-D-Φ-Φ-E-P-V-T-Y sequence motif of MCU pore forms a selectivity filter comprising two acidic rings separated by one helical turn along the central axis of the channel pore. The structure combined with mutagenesis gives insight into the basis of calcium recognition.
Validation ReportPDB-ID: 6dt0

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Jul 11, 2018 / Last update: Jul 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dt0
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8911.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.15 Å/pix.
= 294.4 Å
256 pix
1.15 Å/pix.
= 294.4 Å
256 pix
1.15 Å/pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density
Contour Level:0.07 (by author), 0.06 (movie #1):
Minimum - Maximum-0.15024757 - 0.2846857
Average (Standard dev.)0.00010056752 (0.0074945297)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.-256.0.
Limit255.-1.255.
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.400294.400294.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-25600
NC/NR/NS256256256
D min/max/mean-0.1500.2850.000

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Supplemental data

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Sample components

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Entire Mitochondrial Calcium Uniporter

EntireName: Mitochondrial Calcium Uniporter / Number of components: 3

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Component #1: protein, Mitochondrial Calcium Uniporter

ProteinName: Mitochondrial Calcium Uniporter / Recombinant expression: No
SourceSpecies: Neurospora crassa (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Mitochondrial calcium uniporter

ProteinName: Mitochondrial calcium uniporter / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 52.948117 kDa
SourceSpecies: Neurospora crassa (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.2 mg/ml / pH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: 4 second blot time.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 36000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 36537
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Overall bvalue: 1
Output model

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