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- PDB-6d80: Cryo-EM structure of the mitochondrial calcium uniporter from N. ... -

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Database: PDB / ID: 6d80
TitleCryo-EM structure of the mitochondrial calcium uniporter from N. fischeri bound to saposin
  • Mitochondrial calcium uniporter
  • Saposin A
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 sourceHomo sapiens (human)
Aspergillus fischeri (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5 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 18, 2018Structure modelData collection / Data processingem_3d_reconstruction_em_3d_reconstruction.resolution
1.2Jul 25, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.3Aug 1, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

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Deposited unit
F: Saposin A
H: Saposin A
G: Saposin A
I: Saposin A
J: Saposin A
K: Saposin A
A: Mitochondrial calcium uniporter
B: Mitochondrial calcium uniporter
C: Mitochondrial calcium uniporter
D: Mitochondrial calcium uniporter
hetero molecules

Theoretical massNumber of molelcules
Total (without water)233,22111

  • idetical with deposited unit
  • defined by author
  • Evidence: none, Assembly of the saposin A molecules was determined based on clear electron density in the cryo-EM map, low pass-filtered to 5 Angstrom resolution using the crystal structure of saposin A (PDB ID: 2DOB) as the starting model for model building and refinement.
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)13970
ΔGint (kcal/M)-91
Surface area (Å2)95800


#1: Protein/peptide
Saposin A

Mass: 6911.511 Da / Num. of mol.: 6 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

IDNameTypeEntity IDParent IDSource
1Mitochondrial calcium uniporter / saposin complexORGANELLE OR CELLULAR COMPONENT1,20MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
2336630Aspergillus fischeri (mold)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12469008Escherichia coli BL21(DE3) (bacteria)
23469008Escherichia 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
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

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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: Volta phase plate


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Category: image acquisition
3D reconstructionResolution: 5 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 83343 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00711474
ELECTRON MICROSCOPYf_angle_d1.09515630
ELECTRON MICROSCOPYf_dihedral_angle_d10.8746880
ELECTRON MICROSCOPYf_chiral_restr0.0561834
ELECTRON MICROSCOPYf_plane_restr0.0072042

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