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- EMDB-22042: MCU-EMRE complex of a metazoan mitochondrial calcium uniporter -

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Basic information

Entry
Database: EMDB / ID: EMD-22042
TitleMCU-EMRE complex of a metazoan mitochondrial calcium uniporter
Map datasharpened map
Sample
  • Complex: Mitochondrial Calcium Uniporter (MCU) in complex with EMRE. Embedded in lipid nanodiscs containing cardiolipin.
    • Protein or peptide: Calcium uniporter protein,Protein EMRE homolog, mitochondrial-like Protein fusion
  • Ligand: CALCIUM ION
Keywordsion channel / calcium channel / mitochondrial calcium uniporter / MCU / EMRE / mitochondria / MEMBRANE PROTEIN
Function / homology
Function and homology information


uniporter activity / uniplex complex / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium channel activity / metal ion 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 speciesTribolium castaneum (red flour beetle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLong SB / Wang C
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: J Mol Biol / Year: 2020
Title: Structure and Reconstitution of an MCU-EMRE Mitochondrial Ca Uniporter Complex.
Authors: Chongyuan Wang / Rozbeh Baradaran / Stephen Barstow Long /
Abstract: The proteins MCU and EMRE form the minimal functional unit of the mitochondrial calcium uniporter complex in metazoans, a highly selective and tightly controlled Ca channel of the inner mitochondrial ...The proteins MCU and EMRE form the minimal functional unit of the mitochondrial calcium uniporter complex in metazoans, a highly selective and tightly controlled Ca channel of the inner mitochondrial membrane that regulates cellular metabolism. Here we present functional reconstitution of an MCU-EMRE complex from the red flour beetle, Tribolium castaneum, and a cryo-EM structure of the complex at 3.5 Å resolution. Using a novel assay, we demonstrate robust Ca uptake into proteoliposomes containing the purified complex. Uptake is dependent on EMRE and also on the mitochondrial lipid cardiolipin. The structure reveals a tetrameric channel with a single ion pore. EMRE is located at the periphery of the transmembrane domain and associates primarily with the first transmembrane helix of MCU. Coiled-coil and juxtamembrane domains within the matrix portion of the complex adopt markedly different conformations than in a structure of a human MCU-EMRE complex, suggesting that the structures represent different conformations of these functionally similar metazoan channels.
History
DepositionMay 22, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing 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
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x4s
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22042.png

Downloads & links

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Map

FileDownload / File: emd_22042.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 304 pix.
= 330.752 Å		1.09 Å/pix.
x 304 pix.
= 330.752 Å		1.09 Å/pix.
x 304 pix.
= 330.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.06089739 - 0.10677314
Average (Standard dev.)0.00008087569 (±0.0015306354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 330.752 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z330.752330.752330.752
α/β/γ90.00090.00090.000
start NX/NY/NZ13112264
NX/NY/NZ123151209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0610.1070.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_22042_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial Calcium Uniporter (MCU) in complex with EMRE. Embed...

EntireName: Mitochondrial Calcium Uniporter (MCU) in complex with EMRE. Embedded in lipid nanodiscs containing cardiolipin.
Components
  • Complex: Mitochondrial Calcium Uniporter (MCU) in complex with EMRE. Embedded in lipid nanodiscs containing cardiolipin.
    • Protein or peptide: Calcium uniporter protein,Protein EMRE homolog, mitochondrial-like Protein fusion
  • Ligand: CALCIUM ION

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Supramolecule #1: Mitochondrial Calcium Uniporter (MCU) in complex with EMRE. Embed...

SupramoleculeName: Mitochondrial Calcium Uniporter (MCU) in complex with EMRE. Embedded in lipid nanodiscs containing cardiolipin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tribolium castaneum (red flour beetle)

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Macromolecule #1: Calcium uniporter protein,Protein EMRE homolog, mitochondrial-lik...

MacromoleculeName: Calcium uniporter protein,Protein EMRE homolog, mitochondrial-like Protein fusion
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Tribolium castaneum (red flour beetle)
Molecular weightTheoretical: 27.530723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPTAAALERL TTEEVQGLSD VKTLVNQLYE ALNVREHQLQ KEVELTTQLE TLQQELLPLE EKKLELEQVA NRRSNWMAWA GLGLMSVQF GILARLTWWE YSWDIMEPVT YFVTYGTAMA AYAYFVLTRE EYILNDVRDR QQLLLLHKKA KKTGFDVNQY N VLKDQIAK ...String:
GPTAAALERL TTEEVQGLSD VKTLVNQLYE ALNVREHQLQ KEVELTTQLE TLQQELLPLE EKKLELEQVA NRRSNWMAWA GLGLMSVQF GILARLTWWE YSWDIMEPVT YFVTYGTAMA AYAYFVLTRE EYILNDVRDR QQLLLLHKKA KKTGFDVNQY N VLKDQIAK LELDLKRLRD PLKLRLPPKA AASGSGSGEN LYFQGSGGLL PEPHRTSFGI IRLILTVVPG LLIGAAISKN IA NFL

UniProtKB: Calcium uniporter protein, mitochondrial, Essential MCU regulator, mitochondrial

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / 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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
1.0 mMCaCl2calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot, blot force of 0.
DetailsMonodisperse sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 3 / Number real images: 8143 / Average exposure time: 0.25 sec. / Average electron dose: 1.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4460801
Startup modelType of model: INSILICO MODEL
In silico model: Ab-initio model created using CryoSPARC v2.12
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 52493
Initial angle assignmentType: RANDOM ASSIGNMENT
Software: (Name: cryoSPARC (ver. v2.12.4), RELION (ver. 3.0))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 1 / Avg.num./class: 52493 / Software - Name: cryoSPARC (ver. v2.12.4)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 127 / Target criteria: Correlation coefficient
Output model

PDB-6x4s:
MCU-EMRE complex of a metazoan mitochondrial calcium uniporter

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