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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: 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
SampleMitochondrial calcium uniporter / saposin complex:
saposinProsaposin / (Mitochondrial calcium ...) x 2 / Saposin A / ligand
Function / homologyCalcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / mitochondrial calcium ion homeostasis / mitochondrion / integral component of membrane / Uncharacterized protein
Function and homology information
SourceHomo sapiens (human) / Aspergillus fischeri (mold)
Methodsingle particle reconstruction / cryo EM / 5 Å resolution
AuthorsNguyen NX / Armache JP / Cheng Y / Bai XC
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
Validation ReportPDB-ID: 6d80

SummaryFull reportAbout validation report
DateDeposition: Apr 25, 2018 / Header (metadata) release: May 9, 2018 / Map release: Jul 11, 2018 / Last update: Aug 1, 2018

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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

Downloads & links

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Map

Fileemd_7828.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
0.84 Å/pix.
= 184.8 Å
220 pix
0.84 Å/pix.
= 184.8 Å
220 pix
0.84 Å/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
Contour Level:0.009 (by author), 0.009 (movie #1):
Minimum - Maximum-0.006093651 - 0.021429818
Average (Standard dev.)0.0003616772 (0.0017737029)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin0.0.0.
Limit219.219.219.
Spacing220220220
CellA=B=C: 184.79999 Å
α=β=γ: 90.0 deg.

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/NZ
NX/NY/NZ
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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Sample components

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Entire Mitochondrial calcium uniporter / saposin complex

EntireName: Mitochondrial calcium uniporter / saposin complex / Number of components: 6

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Component #1: cellular-component, Mitochondrial calcium uniporter / saposin complex

Cellular-componentName: Mitochondrial calcium uniporter / saposin complex / Recombinant expression: No

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Component #2: protein, saposin

ProteinName: saposinProsaposin / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: cellular-component, Mitochondrial calcium uniporter

Cellular-componentName: Mitochondrial calcium uniporter / Recombinant expression: No
SourceSpecies: Aspergillus fischeri (mold)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #4: protein, Saposin A

ProteinName: Saposin A / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.911511 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #5: protein, Mitochondrial calcium uniporter

ProteinName: Mitochondrial calcium uniporter / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.928004 kDa
SourceSpecies: Aspergillus fischeri (mold)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #6: 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.: 0.6 mg/ml
Buffer solution: 20 mM HEPES, pH 7.5, 300 mM sodium chloride, 1 mM calcium chloride, 2% glycerol
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 83343
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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