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- EMDB-22290: Structure of a mitochondrial calcium uniporter holocomplex (MICU1... -

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Basic information

Entry
Database: EMDB / ID: EMD-22290
TitleStructure of a mitochondrial calcium uniporter holocomplex (MICU1, MICU2, MCU, EMRE) in low Ca2+
Map data
SampleMitochondrial Calcium Uniporter holocomplex
  • EMRE
  • MCU
  • MICU1-MICU2 heterodimer
  • Protein EMRE homolog, mitochondrial-like Protein
  • Calcium uniporter protein
  • (Calcium uptake protein ...) x 2
  • ligand
Function / homology
Function and homology information


regulation of cellular hyperosmotic salinity response / negative regulation of mitochondrial calcium ion concentration / uniplex complex / calcium import into the mitochondrion / uniporter activity / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / integral component of mitochondrial membrane / integral component of mitochondrial inner membrane ...regulation of cellular hyperosmotic salinity response / negative regulation of mitochondrial calcium ion concentration / uniplex complex / calcium import into the mitochondrion / uniporter activity / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / integral component of mitochondrial membrane / integral component of mitochondrial inner membrane / calcium ion import / intracellular / calcium channel complex / calcium channel activity / protein homooligomerization / mitochondrial intermembrane space / defense response / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein binding
EF-hand domain / Calcium uptake protein 1/2/3 / MCU family / Essential MCU regulator, mitochondrial / EF-Hand 1, calcium-binding site / EF-hand domain pair / Calcium uniporter protein, C-terminal
Calcium uniporter protein / Protein EMRE homolog, mitochondrial-like Protein / Calcium uptake protein 2, mitochondrial / Calcium uptake protein 1, mitochondrial
Biological speciesTribolium castaneum (red flour beetle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLong SB / Wang C / Baradaran R / Jacewicz A / Delgado B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131921 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
CitationJournal: Elife / Year: 2020
Title: Structures reveal gatekeeping of the mitochondrial Ca uniporter by MICU1-MICU2.
Authors: Chongyuan Wang / Agata Jacewicz / Bryce D Delgado / Rozbeh Baradaran / Stephen Barstow Long /
Abstract: The mitochondrial calcium uniporter is a Ca-gated ion channel complex that controls mitochondrial Ca entry and regulates cell metabolism. MCU and EMRE form the channel while Ca-dependent regulation ...The mitochondrial calcium uniporter is a Ca-gated ion channel complex that controls mitochondrial Ca entry and regulates cell metabolism. MCU and EMRE form the channel while Ca-dependent regulation is conferred by MICU1 and MICU2 through an enigmatic process. We present a cryo-EM structure of an MCU-EMRE-MICU1-MICU2 holocomplex comprising MCU and EMRE subunits from the beetle Tribolium castaneum in complex with a human MICU1-MICU2 heterodimer at 3.3 Å resolution. With analogy to how neuronal channels are blocked by protein toxins, a uniporter interaction domain on MICU1 binds to a channel receptor site comprising MCU and EMRE subunits to inhibit ion flow under resting Ca conditions. A Ca-bound structure of MICU1-MICU2 at 3.1 Å resolution indicates how Ca-dependent changes enable dynamic response to cytosolic Ca signals.
Validation ReportPDB-ID: 6xqn

SummaryFull reportAbout validation report
History
DepositionJul 9, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xqn
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xqn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22290.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 319.2 Å
1.06 Å/pix.
x 300 pix.
= 319.2 Å
1.06 Å/pix.
x 300 pix.
= 319.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.031599887 - 0.05272293
Average (Standard dev.)0.0000647780 (±0.0008696453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 319.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z319.200319.200319.200
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0970.154-0.000

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Supplemental data

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Additional map: sharpened map calculated from the first 6 frames.

Fileemd_22290_additional_1.map
Annotationsharpened map calculated from the first 6 frames.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: unsharpened map

Fileemd_22290_additional_2.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Mitochondrial Calcium Uniporter holocomplex

EntireName: Mitochondrial Calcium Uniporter holocomplex / Number of components: 9

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Component #1: protein, Mitochondrial Calcium Uniporter holocomplex

ProteinName: Mitochondrial Calcium Uniporter holocomplex / Recombinant expression: No

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Component #2: protein, EMRE

ProteinName: EMRE / Recombinant expression: No
SourceSpecies: Tribolium castaneum (red flour beetle)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Expi293, Invitrogen

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Component #3: protein, MCU

ProteinName: MCU / Recombinant expression: No
SourceSpecies: Tribolium castaneum (red flour beetle)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Expi293, Invitrogen

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Component #4: protein, MICU1-MICU2 heterodimer

ProteinName: MICU1-MICU2 heterodimer / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Expi293, Invitrogen

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Component #5: protein, Protein EMRE homolog, mitochondrial-like Protein

ProteinName: Protein EMRE homolog, mitochondrial-like Protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 7.37219 kDa
SourceSpecies: Tribolium castaneum (red flour beetle)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Calcium uniporter protein

ProteinName: Calcium uniporter protein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 23.6341 kDa
SourceSpecies: Tribolium castaneum (red flour beetle)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Calcium uptake protein 1, mitochondrial

ProteinName: Calcium uptake protein 1, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.422883 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, Calcium uptake protein 2, mitochondrial

ProteinName: Calcium uptake protein 2, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.980609 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: 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.: 1 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: 71 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: -1000.0 - -3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 21115

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 350160
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.3 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: 124
Output model

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