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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 / homologyCalcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / mitochondrial calcium ion homeostasis / mitochondrion / integral component of membrane / Uncharacterized protein
Function and homology information
Specimen sourceAspergillus fischeri (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsNguyen, N.X. / Armache, J.P. / Cheng, Y. / Bai, X.C.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 25, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Jul 25, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Aug 1, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

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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
Polyers191,7124
Non-polymers401
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)11740
ΔGint (kcal/M)-74
Surface area (Å2)68720

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Components

#1: Protein/peptide
Mitochondrial calcium uniporter /


Mass: 47928.004 Da / Num. of mol.: 4 / 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 / Formula: Ca / Calcium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 solutionDetails: 20 mM HEPES, pH 7.5, 300 mM sodium chloride, 1 mM calcium chloride, 2% glycerol
pH: 7.5
SpecimenConc.: 0.6 mg/ml
Details: N. fischeri MCU was reconstituted into lipid using E. coli total lipids and human saposin A as the membrane scaffolding protein.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number 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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