[English] 日本語
Yorodumi
- EMDB-8911: Cryo-EM structure of a mitochondrial calcium uniporter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8911
TitleCryo-EM structure of a mitochondrial calcium uniporter
Map dataSingle-particle cryo-EM reconstruction of the N. crassa mitochondrial calcium uniporter
Sample
  • Complex: Mitochondrial Calcium Uniporter
    • Protein or peptide: Mitochondrial calcium uniporter
  • Ligand: CALCIUM ION
Keywordsmitochondrial calcium uniporter / calcium-selective ion channel / calcium uptake / uniporter / TRANSPORT 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 speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYoo J / Wu M
CitationJournal: Science / Year: 2018
Title: Cryo-EM structure of a mitochondrial calcium uniporter.
Authors: Jiho Yoo / Mengyu Wu / Ying Yin / Mark A Herzik / Gabriel C Lander / Seok-Yong Lee /
Abstract: Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary ...Calcium transport plays an important role in regulating mitochondrial physiology and pathophysiology. The mitochondrial calcium uniporter (MCU) is a calcium-selective ion channel that is the primary mediator for calcium uptake into the mitochondrial matrix. Here, we present the cryo-electron microscopy structure of the full-length MCU from to an overall resolution of ~3.7 angstroms. Our structure reveals a tetrameric architecture, with the soluble and transmembrane domains adopting different symmetric arrangements within the channel. The conserved W-D-Φ-Φ-E-P-V-T-Y sequence motif of MCU pore forms a selectivity filter comprising two acidic rings separated by one helical turn along the central axis of the channel pore. The structure combined with mutagenesis gives insight into the basis of calcium recognition.
History
DepositionJun 14, 2018-
Header (metadata) releaseJul 4, 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: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6dt0
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8911.png

Downloads & links

-
Map

FileDownload / File: emd_8911.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle cryo-EM reconstruction of the N. crassa mitochondrial calcium uniporter
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.06
Minimum - Maximum-0.15024757 - 0.2846857
Average (Standard dev.)0.00010056752 (±0.0074945297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-2560
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.400294.400294.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-25600
NC/NR/NS256256256
D min/max/mean-0.1500.2850.000

-
Supplemental data

-
Half map: N. crassa mitochondrial calcium uniporter, half map 1

Fileemd_8911_half_map_1.map
AnnotationN. crassa mitochondrial calcium uniporter, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: N. crassa mitochondrial calcium uniporter, half map 2

Fileemd_8911_half_map_2.map
AnnotationN. crassa mitochondrial calcium uniporter, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mitochondrial Calcium Uniporter

EntireName: Mitochondrial Calcium Uniporter
Components
  • Complex: Mitochondrial Calcium Uniporter
    • Protein or peptide: Mitochondrial calcium uniporter
  • Ligand: CALCIUM ION

-
Supramolecule #1: Mitochondrial Calcium Uniporter

SupramoleculeName: Mitochondrial Calcium Uniporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neurospora crassa (fungus)

-
Macromolecule #1: Mitochondrial calcium uniporter

MacromoleculeName: Mitochondrial calcium uniporter / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 52.948117 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASTSVSPKT RETEAEAKAK KLDQKRLDEH EEEVRAREQQ VRRPWHREGA DKPPVEGNAD PIAKGKLLTT PTRLLKLILP LPLRVEKDQ KNNGRNNEYG RSISLNSDIQ PLALLIHPQQ PLSYVERLIQ AELPPVVENG QEKIPNVYFR AEDSEQGDQK P TSRAEARS ...String:
MASTSVSPKT RETEAEAKAK KLDQKRLDEH EEEVRAREQQ VRRPWHREGA DKPPVEGNAD PIAKGKLLTT PTRLLKLILP LPLRVEKDQ KNNGRNNEYG RSISLNSDIQ PLALLIHPQQ PLSYVERLIQ AELPPVVENG QEKIPNVYFR AEDSEQGDQK P TSRAEARS KDDGGEPSEY NTNLSHVASA SGLGHRGPKR SSQDKRWVRW SSSTEMGDFI RDAARGREFA IEIEGYNIEM RV SVPSFGD RTYYMRQRLR KMSSEIDGLA KIKHECDLLA HRSAHRLAKG GFGLLAGWWG VVYYVTFHTE FGWDLVEPVT YLA GLTTIM GGYLWFLYIN KDLSYKAAMN VTVSRRQHAL YEMKGFDIER WEQLVQDANA LRREIRVIAV EYDVDWDETR DVGE DVKDV LDEERSRRDD EHRSIEKEKD EKFTEDEKRK RKKDKESKET SGDSTNSHHH HHH

UniProtKB: Calcium uniporter protein, mitochondrial

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.2 mg/mL
BufferpH: 8
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER / Details: 4 second blot time.
DetailsFinal reconstruction comprises ~80% of MCU in nanodisc (crosslinked using BS3) and ~20% MCU in amphipol.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3686168
Details: 1,791,114 particles of MCU in amphipol, 1,895,054 particles of crosslinked MCU in nanodisc
Startup modelType of model: OTHER
Details: Ab initio map generated from cryoSPARC, low-passed filtered to 30 Angstrom
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 36537
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementOverall B value: 100
Output model

PDB-6dt0:
Cryo-EM structure of a mitochondrial calcium uniporter

+
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