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- EMDB-0627: Cryo-EM map of human MCU -

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Basic information

Entry
Database: EMDB / ID: EMD-0627
TitleCryo-EM map of human MCU
Map data
SampleMCU
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsWang Y / Bai X / Jiang Y
CitationJournal: Cell / Year: 2019
Title: Structural Mechanism of EMRE-Dependent Gating of the Human Mitochondrial Calcium Uniporter.
Authors: Yan Wang / Nam X Nguyen / Ji She / Weizhong Zeng / Yi Yang / Xiao-Chen Bai / Youxing Jiang /
Abstract: Mitochondrial calcium uptake is crucial to the regulation of eukaryotic Ca homeostasis and is mediated by the mitochondrial calcium uniporter (MCU). While MCU alone can transport Ca in primitive ...Mitochondrial calcium uptake is crucial to the regulation of eukaryotic Ca homeostasis and is mediated by the mitochondrial calcium uniporter (MCU). While MCU alone can transport Ca in primitive eukaryotes, metazoans require an essential single membrane-spanning auxiliary component called EMRE to form functional channels; however, the molecular mechanism of EMRE regulation remains elusive. Here, we present the cryo-EM structure of the human MCU-EMRE complex, which defines the interactions between MCU and EMRE as well as pinpoints the juxtamembrane loop of MCU and extended linker of EMRE as the crucial elements in the EMRE-dependent gating mechanism among metazoan MCUs. The structure also features the dimerization of two MCU-EMRE complexes along an interface at the N-terminal domain (NTD) of human MCU that is a hotspot for post-translational modifications. Thus, the human MCU-EMRE complex, which constitutes the minimal channel components among metazoans, provides a framework for future mechanistic studies on MCU.
DateDeposition: Mar 1, 2019 / Header (metadata) release: Mar 27, 2019 / Map release: May 22, 2019 / Update: May 29, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_0627.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 180 pix.
= 192.6 Å
1.07 Å/pix.
x 180 pix.
= 192.6 Å
1.07 Å/pix.
x 180 pix.
= 192.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.061015815 - 0.108321935
Average (Standard dev.)0.0007231454 (±0.004591557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 192.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z192.600192.600192.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0610.1080.001

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Supplemental data

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Sample components

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Entire MCU

EntireName: MCU / Number of components: 2

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Component #1: protein, MCU

ProteinName: MCU / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, MCU

ProteinName: MCU / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

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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: 2.2 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: 93255
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF

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