[English] 日本語
Yorodumi
- EMDB-7971: cryo-EM structure of the mitochondrial calcium uniporter MCU from... -

+
Open data


ID or keywords:

Loading...

-
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 / identical protein binding / metal ion 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

-
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

-
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

-
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

-
Macromolecule #3: CALCIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more