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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 dataApo form of a cation channel
Sample
  • Complex: MCU
    • Protein or peptide: MCU
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 / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis ...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 / 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 / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / glucose homeostasis / mitochondrial inner membrane / mitochondrion / identical protein binding
Similarity search - Function
Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
Calcium uniporter protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsWang Y / Bai X / Jiang Y
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-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0627.png

Downloads & links

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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)
AnnotationApo form of a cation channel
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

Histogram

Histogram (log scale)
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
Components
  • Complex: MCU
    • Protein or peptide: MCU

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Supramolecule #1: MCU

SupramoleculeName: MCU / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: MCU

MacromoleculeName: MCU / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

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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: 2.2 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93255
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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