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- EMDB-7971: Cryo-EM structure of the mitochondrial calcium uniporter MCU from... -

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Basic information

Entry
Database: EMDB / ID: 7971
TitleCryo-EM structure of the mitochondrial calcium uniporter MCU from the fungus Cyphellophora europaea
Map dataCryo-EM structure of the mitochondrial calcium uniporter
SampleMitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.:
Mitochondrial calcium uniporter MCU / (ligand) x 2
Function / homologyCalcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / mitochondrial calcium ion homeostasis / mitochondrion / integral component of membrane / identical protein binding / Uncharacterized protein
Function and homology information
SourceCyphellophora europaea (fungus) / Cyphellophora europaea CBS 101466 (fungus)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsLong SB / Baradaran R / Wang C
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters.
Authors: Rozbeh Baradaran / Chongyuan Wang / Andrew Francis Siliciano / Stephen Barstow Long
Validation ReportPDB-ID: 6dnf

SummaryFull reportAbout validation report
DateDeposition: Jun 6, 2018 / Header (metadata) release: Jun 27, 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: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dnf
  • Surface level: 2.8
  • 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_7971.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
0.86 Å/pix.
= 330.624 Å
384 pix
0.86 Å/pix.
= 330.624 Å
384 pix
0.86 Å/pix.
= 330.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density
Contour Level:2.8 (by author), 2.8 (movie #1):
Minimum - Maximum-9.453419 - 18.241378999999998
Average (Standard dev.)-0.0019589954 (0.45630026)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.0.0.
Limit383.383.383.
Spacing384384384
CellA=B=C: 330.624 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8610.8610.861
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z330.624330.624330.624
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-9.45318.241-0.002

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Supplemental data

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Sample components

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Entire Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellopho...

EntireName: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.
Number of components: 4

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Component #1: cellular-component, Mitochondrial Calcium Uniporter (MCU) from th...

Cellular-componentName: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.
Recombinant expression: No
MassTheoretical: 158.328 kDa
SourceSpecies: Cyphellophora europaea (fungus)
Source (engineered)Expression System: Komagataella pastoris (fungus)

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Component #2: protein, Mitochondrial calcium uniporter MCU

ProteinName: Mitochondrial calcium uniporter MCU / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 39.637176 kDa
SourceSpecies: Cyphellophora europaea CBS 101466 (fungus)
Source (engineered)Expression System: Komagataella pastoris (fungus)

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Component #3: ligand, 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTAN...

LigandName: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.734981 kDa

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Component #4: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 3 / 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.: 5 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 % / Details: 2 second blot, blot force of 0.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000. X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 6040

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 376541
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 136.580000000000013
Output model

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