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- EMDB-7971: cryo-EM structure of the mitochondrial calcium uniporter MCU from... -

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Basic information

Entry
Database: EMDB / ID: EMD-7971
Titlecryo-EM structure of the mitochondrial calcium uniporter MCU from the fungus Cyphellophora europaea
Map dataCryo-EM structure of the mitochondrial calcium uniporter
Sample
  • Organelle or cellular component: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.
    • Protein or peptide: Mitochondrial calcium uniporter MCU
  • Ligand: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
  • Ligand: CALCIUM ION
Keywordsmitochondria / calcium / ion channel / eukaryotic / MEMBRANE PROTEIN
Function / homology
Function and homology information


uniporter activity / uniplex complex / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium channel activity / protein homotetramerization / mitochondrial inner membrane / metal ion binding / 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 speciesCyphellophora europaea (fungus) / Cyphellophora europaea CBS 101466 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLong SB / Baradaran R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094273 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters.
Authors: Rozbeh Baradaran / Chongyuan Wang / Andrew Francis Siliciano / Stephen Barstow Long /
Abstract: The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel and a major route of calcium entry into mitochondria. How the channel catalyses ion permeation and achieves ...The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel and a major route of calcium entry into mitochondria. How the channel catalyses ion permeation and achieves ion selectivity are not well understood, partly because MCU is thought to have a distinct architecture in comparison to other cellular channels. Here we report cryo-electron microscopy reconstructions of MCU channels from zebrafish and Cyphellophora europaea at 8.5 Å and 3.2 Å resolutions, respectively. In contrast to a previous report of pentameric stoichiometry for MCU, both channels are tetramers. The atomic model of C. europaea MCU shows that a conserved WDXXEP signature sequence forms the selectivity filter, in which calcium ions are arranged in single file. Coiled-coil legs connect the pore to N-terminal domains in the mitochondrial matrix. In C. europaea MCU, the N-terminal domains assemble as a dimer of dimers; in zebrafish MCU, they form an asymmetric crescent. The structures define principles that underlie ion permeation and calcium selectivity in this unusual channel.
History
DepositionJun 6, 2018-
Header (metadata) releaseJun 27, 2018-
Map releaseJul 11, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6dnf
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7971.png

Downloads & links

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Map

FileDownload / File: emd_7971.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the mitochondrial calcium uniporter
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.624 Å		0.86 Å/pix.
x 384 pix.
= 330.624 Å		0.86 Å/pix.
x 384 pix.
= 330.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.8
Minimum - Maximum-9.453419 - 18.241378999999998
Average (Standard dev.)-0.0019589954 (±0.45630026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.624 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8610.8610.861
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z330.624330.624330.624
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-9.45318.241-0.002

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Supplemental data

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Sample components

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Entire : Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellopho...

EntireName: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.
Components
  • Organelle or cellular component: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.
    • Protein or peptide: Mitochondrial calcium uniporter MCU
  • Ligand: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
  • Ligand: CALCIUM ION

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Supramolecule #1: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellopho...

SupramoleculeName: Mitochondrial Calcium Uniporter (MCU) from the fungus Cyphellophora europaea.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Cyphellophora europaea (fungus)
Molecular weightTheoretical: 158.328 KDa

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Macromolecule #1: Mitochondrial calcium uniporter MCU

MacromoleculeName: Mitochondrial calcium uniporter MCU / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyphellophora europaea CBS 101466 (fungus)
Molecular weightTheoretical: 39.637176 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MTKGKLLTTP SRLLKLVLPL STVDHNTDRK DVAPLALLVH PQQPLSYLER LIQAELPPPD PQDSKSTTRS VTFRAMEAKD DEIKPRKKA DTEGGGGSDG SVQSYSGAGR EGEGKDEGEF VRWSPSTEIG DFIRDAARAK EFEVEIEGSP GVIKVAVPSF N DRTYYLRQ ...String:
MTKGKLLTTP SRLLKLVLPL STVDHNTDRK DVAPLALLVH PQQPLSYLER LIQAELPPPD PQDSKSTTRS VTFRAMEAKD DEIKPRKKA DTEGGGGSDG SVQSYSGAGR EGEGKDEGEF VRWSPSTEIG DFIRDAARAK EFEVEIEGSP GVIKVAVPSF N DRTYYLRQ RLRRTSRKIS KLAAIKEECD KAAHRGAQRI ALAGCGGLIG YWYIVYRLTF ETDLGWDVME PVTYLVGLST LI GGYMWFL WHNREVSYRS ALNITVSARQ NKLYQAKGFS LQDWEGYLEE ANAMRREIKA VASEYDVDWN ETQDEGGDEK VTK ALRDER KNNNGTKNKS KEGEEDDEDD GEGEEF

UniProtKB: Calcium uniporter protein, mitochondrial

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Macromolecule #2: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]...

MacromoleculeName: 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
type: ligand / ID: 2 / Number of copies: 8 / Formula: DGG
Molecular weightTheoretical: 734.981 Da
Chemical component information

ChemComp-DGG:
1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 3 / 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
0.5 mMdigitonindigitonin
0.05 mg/mLcardiolipin1',3'-bis[1,2-dioleoyl-sn-glycero-3-phospho]-sn-glycerol
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: AIR
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: 6040 / Average exposure time: 0.2 sec. / 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 / Nominal magnification: 29000
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: 547637
Startup modelType of model: INSILICO MODEL / In silico model: Generated using RELION 2.1
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Software - details: cisTEM 1.0 / Number images used: 376541
Initial angle assignmentType: RANDOM ASSIGNMENT / Software:
Namedetails
RELION (ver. 2.1)
FREALIGNcisTEM 1.0
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN (ver. 1.0) / Software - details: cisTEM 1.0
Final 3D classificationNumber classes: 1 / Avg.num./class: 376541 / Software - Name: FREALIGN (ver. 1.0) / Software - details: cisTEM 1.0

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 136.58 / Target criteria: Correlation coefficient
Output model

PDB-6dnf:
Cryo-EM structure of the mitochondrial calcium uniporter MCU from the fungus Cyphellophora europaea

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