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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 / Processing of SMDT1 / positive regulation of mitochondrial calcium ion concentration / 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 / Processing of SMDT1 / positive regulation of mitochondrial calcium ion concentration / 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 / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / glucose homeostasis / protein-macromolecule adaptor activity / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / mitochondrion / 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: Structure / Year: 2026
Title: Matrix polyamines regulate bidirectional calcium flux through MCU.
Authors: Qinzhe Wang / Enrique Balderas / Alejandro Jara Ramos / Ashley Nwafor / Jack S McManus / Neeraj K Rai / Yasmin B Masini / David R Eberhardt / Emma C Rekate / Anthony M Balynas / Xue Yin / ...Authors: Qinzhe Wang / Enrique Balderas / Alejandro Jara Ramos / Ashley Nwafor / Jack S McManus / Neeraj K Rai / Yasmin B Masini / David R Eberhardt / Emma C Rekate / Anthony M Balynas / Xue Yin / Tracy Murray Stewart / Erhu Cao / Anna Stary-Weinzinger / Dipayan Chaudhuri /
Abstract: Polyamines, well-known regulators of the mitochondrial calcium (Ca) uniporter channel, show unexpected effects when binding the channel from within the matrix. Using cryo-EM, molecular dynamics ...Polyamines, well-known regulators of the mitochondrial calcium (Ca) uniporter channel, show unexpected effects when binding the channel from within the matrix. Using cryo-EM, molecular dynamics simulations, and mutagenesis experiments, we determine that polyamines achieve such regulation by binding within the pore to a ring of negative residues forming a matrix gate, inhibiting Ca conduction. In whole-mitoplast electrophysiology assays, matrix polyamines cause a gradual increase in Ca currents during prolonged conduction, due to relief of this inhibition. Notably, this electrostatic binding increases 3-fold as the inner membrane depolarizes, preventing Ca efflux. Additionally, we also identify that phospholipids form part of the Ca conduction pathway through MCU. Because we find significant variability in matrix polyamine content across mouse organs, this unexpected mechanism for sculpting the mitochondrial Ca waveform suggests a tissue-specific regulation of metabolism.
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
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Revision 1.1Aug 12, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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