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- PDB-13io: MCU-EMRE complex with spermine -

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Basic information

Entry
Database: PDB / ID: 13io
TitleMCU-EMRE complex with spermine
Components
  • Calcium uniporter protein, mitochondrial
  • Essential MCU regulator, mitochondrial
KeywordsMEMBRANE PROTEIN / mitochondrial calcium uniporter / MCU / EMRE
Function / homology
Function and homology information


uniporter activity / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Processing of SMDT1 / Mitochondrial calcium ion transport / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / channel activator activity / cellular response to calcium ion starvation ...uniporter activity / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Processing of SMDT1 / Mitochondrial calcium ion transport / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / channel activator activity / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / protein complex oligomerization / calcium channel complex / Mitochondrial protein degradation / generation of precursor metabolites and energy / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / cell migration / glucose homeostasis / protein-macromolecule adaptor activity / cell population proliferation / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Essential MCU regulator, mitochondrial / Putative mitochondrial precursor protein / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
CARDIOLIPIN / Chem-P5S / SPERMINE / Calcium uniporter protein, mitochondrial / Essential MCU regulator, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWang, Q. / Balderas, E. / Rai, N.K. / Cao, E. / Chaudhuri, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL165797 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL141353 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01DK143101 United States
CitationJournal: To Be Published
Title: MCU-EMRE complex with spermine
Authors: Wang, Q. / Balderas, E. / Rai, N.K. / Cao, E. / Chaudhuri, D.
History
DepositionMay 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Essential MCU regulator, mitochondrial
B: Essential MCU regulator, mitochondrial
C: Essential MCU regulator, mitochondrial
D: Essential MCU regulator, mitochondrial
E: Calcium uniporter protein, mitochondrial
F: Calcium uniporter protein, mitochondrial
G: Calcium uniporter protein, mitochondrial
H: Calcium uniporter protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,77419
Polymers105,4678
Non-polymers9,30711
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Essential MCU regulator, mitochondrial / Single-pass membrane protein with aspartate-rich tail 1 / mitochondrial


Mass: 5864.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMDT1, C22orf32, EMRE / Production host: Homo sapiens (human) / References: UniProt: Q9H4I9
#2: Protein
Calcium uniporter protein, mitochondrial / HsMCU / Coiled-coil domain-containing protein 109A


Mass: 20502.756 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Production host: Homo sapiens (human) / References: UniProt: Q8NE86

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Non-polymers , 4 types, 11 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO10P
#5: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#6: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: MCU-EMRE complex with spermine / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX2.0_5848model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84413 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE

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