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- EMDB-0625: Human MCU-EMRE complex, dimer of channel -

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Basic information

Entry
Database: EMDB / ID: EMD-0625
TitleHuman MCU-EMRE complex, dimer of channel
Map data
SampleMCU/EMRE complex
  • Calcium uniporter protein, mitochondrial
  • Essential MCU regulator, mitochondrial
  • ligand
Function / homology
Function and homology information


Mitochondrial calcium ion transport / Processing of SMDT1 / uniplex complex / calcium import into the mitochondrion / mitochondrial calcium ion transmembrane transport / uniporter activity / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / integral component of mitochondrial inner membrane / positive regulation of insulin secretion ...Mitochondrial calcium ion transport / Processing of SMDT1 / uniplex complex / calcium import into the mitochondrion / mitochondrial calcium ion transmembrane transport / uniporter activity / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / integral component of mitochondrial inner membrane / positive regulation of insulin secretion / calcium channel activity / calcium channel complex / calcium-mediated signaling / glucose homeostasis / mitochondrial inner membrane / protein complex oligomerization / mitochondrial matrix / mitochondrion / identical protein binding / nucleus
Putative mitochondrial precursor protein / Mitochondrial calcium uniporter / MCU family / Essential MCU regulator, mitochondrial / Calcium uniporter protein, C-terminal
Calcium uniporter protein, mitochondrial / Essential MCU regulator, mitochondrial
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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.
Validation ReportPDB-ID: 6o58

SummaryFull reportAbout validation report
History
DepositionMar 1, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMay 22, 2019-
UpdateMay 29, 2019-
Current statusMay 29, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6o58
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0625.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.)
0.84 Å/pix.
x 300 pix.
= 252. Å
0.84 Å/pix.
x 300 pix.
= 252. Å
0.84 Å/pix.
x 300 pix.
= 252. 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 LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.02369144 - 0.05746298
Average (Standard dev.)0.00048393483 (±0.0037649993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0240.0570.000

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Supplemental data

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Sample components

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Entire MCU/EMRE complex

EntireName: MCU/EMRE complex / Number of components: 4

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Component #1: protein, MCU/EMRE complex

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

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Component #2: protein, Calcium uniporter protein, mitochondrial

ProteinName: Calcium uniporter protein, mitochondrial / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 39.920828 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Essential MCU regulator, mitochondrial

ProteinName: Essential MCU regulator, mitochondrial / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 11.45414 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 2 / 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 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 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: 30979
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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