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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 dataDimerized form of a cation channel
Sample
  • Complex: MCU/EMRE complex
    • Protein or peptide: Calcium uniporter protein, mitochondrial
    • Protein or peptide: Essential MCU regulator, mitochondrial
  • Ligand: CALCIUM ION
Keywordsion channel / complex / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / channel activator activity / calcium import into the mitochondrion / cellular response to calcium ion starvation ...uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / channel activator activity / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / protein complex oligomerization / calcium channel complex / Mitochondrial protein degradation / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / glucose homeostasis / protein-macromolecule adaptor activity / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Essential MCU regulator, mitochondrial / Putative mitochondrial precursor protein / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
Calcium uniporter protein, mitochondrial / Essential MCU regulator, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang Y / Bai X
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
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.
History
DepositionMar 1, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMay 22, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing 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
  • Download
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0625.png

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)
AnnotationDimerized form of a cation channel
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

Histogram

Histogram (log scale)
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
Components
  • Complex: MCU/EMRE complex
    • Protein or peptide: Calcium uniporter protein, mitochondrial
    • Protein or peptide: Essential MCU regulator, mitochondrial
  • Ligand: CALCIUM ION

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Supramolecule #1: MCU/EMRE complex

SupramoleculeName: MCU/EMRE complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium uniporter protein, mitochondrial

MacromoleculeName: Calcium uniporter protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.920828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAGRSLL LLLSSRGGGG GGAGGCGALT AGCFPGLGVS RHRQQQHHRT VHQRIASWQN LGAVYCSTVV PSDDVTVVYQ NGLPVISVR LPSRRERCQF TLKPISDSVG VFLRQLQEED RGIDRVAIYS PDGVRVAAST GIDLLLLDDF KLVINDLTYH V RPPKRDLL ...String:
MAAAAGRSLL LLLSSRGGGG GGAGGCGALT AGCFPGLGVS RHRQQQHHRT VHQRIASWQN LGAVYCSTVV PSDDVTVVYQ NGLPVISVR LPSRRERCQF TLKPISDSVG VFLRQLQEED RGIDRVAIYS PDGVRVAAST GIDLLLLDDF KLVINDLTYH V RPPKRDLL SHENAATLND VKTLVQQLYT TLCIEQHQLN KERELIERLE DLKEQLAPLE KVRIEISRKA EKRTTLVLWG GL AYMATQF GILARLTWWE YSWDIMEPVT YFITYGSAMA MYAYFVMTRQ EYVYPEARDR QYLLFFHKGA KKSRFDLEKY NQL KDAIAQ AEMDLKRLRD PLQVHLPLRQ IGEKD

UniProtKB: Calcium uniporter protein, mitochondrial

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Macromolecule #2: Essential MCU regulator, mitochondrial

MacromoleculeName: Essential MCU regulator, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.45414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASGAARWLV LAPVRSGALR SGPSLRKDGD VSAAWSGSGR SLVPSRSVIV TRSGAILPKP VKMSFGLLRV FSIVIPFLYV GTLISKNFA ALLEEHDIFV PEDDDDDD

UniProtKB: Essential MCU regulator, mitochondrial

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30979
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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