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- PDB-6d7w: Cryo-EM structure of the mitochondrial calcium uniporter from N. ... -

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Basic information

Entry
Database: PDB / ID: 6d7w
TitleCryo-EM structure of the mitochondrial calcium uniporter from N. fischeri at 3.8 Angstrom resolution
ComponentsMitochondrial calcium uniporter
KeywordsTRANSPORT PROTEIN / Mitochondria / calcium channel
Function / homologyuniporter activity / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / mitochondrial calcium ion homeostasis / calcium channel activity / mitochondrial inner membrane / Calcium uniporter protein
Function and homology information
Biological speciesAspergillus fischeri (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsNguyen, N.X. / Armache, J.-P. / Cheng, Y. / Bai, X.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of a fungal mitochondrial calcium uniporter.
Authors: Nam X Nguyen / Jean-Paul Armache / Changkeun Lee / Yi Yang / Weizhong Zeng / Vamsi K Mootha / Yifan Cheng / Xiao-Chen Bai / Youxing Jiang /
Abstract: The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel localized to the inner mitochondrial membrane. Here, we describe the structure of an MCU orthologue from the fungus ...The mitochondrial calcium uniporter (MCU) is a highly selective calcium channel localized to the inner mitochondrial membrane. Here, we describe the structure of an MCU orthologue from the fungus Neosartorya fischeri (NfMCU) determined to 3.8 Å resolution by phase-plate cryo-electron microscopy. The channel is a homotetramer with two-fold symmetry in its amino-terminal domain (NTD) that adopts a similar structure to that of human MCU. The NTD assembles as a dimer of dimers to form a tetrameric ring that connects to the transmembrane domain through an elongated coiled-coil domain. The ion-conducting pore domain maintains four-fold symmetry, with the selectivity filter positioned at the start of the pore-forming TM2 helix. The aspartate and glutamate sidechains of the conserved DIME motif are oriented towards the central axis and separated by one helical turn. The structure of NfMCU offers insights into channel assembly, selective calcium permeation, and inhibitor binding.
History
DepositionApr 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 1, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Mitochondrial calcium uniporter
C: Mitochondrial calcium uniporter
B: Mitochondrial calcium uniporter
D: Mitochondrial calcium uniporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7525
Polymers191,7124
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11740 Å2
ΔGint-74 kcal/mol
Surface area68720 Å2

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Components

#1: Protein
Mitochondrial calcium uniporter /


Mass: 47928.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fischeri (mold) / Gene: NFIA_105760 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1CWT6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial calcium uniporter / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Aspergillus fischeri (mold)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 20 mM HEPES, pH 7.5, 300 mM sodium chloride, 1 mM calcium chloride, 2% glycerol
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: N. fischeri MCU was reconstituted into lipid using E. coli total lipids and human saposin A as the membrane scaffolding protein.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83343 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089075
ELECTRON MICROSCOPYf_angle_d1.20312281
ELECTRON MICROSCOPYf_dihedral_angle_d9.4335443
ELECTRON MICROSCOPYf_chiral_restr0.0661353
ELECTRON MICROSCOPYf_plane_restr0.0081567

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