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- EMDB-70351: Human MPC1-2 Complex IMS-open (TMs weighted) -

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Basic information

Entry
Database: EMDB / ID: EMD-70351
TitleHuman MPC1-2 Complex IMS-open (TMs weighted)
Map data
Sample
  • Complex: MPC1-2
    • Protein or peptide: Human MPC1
    • Protein or peptide: Human MPC2
KeywordsMEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsQi X / Sun Y / Wang Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230054 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure of human mitochondrial pyruvate carrier MPC1 and MPC2 complex.
Authors: Yingyuan Sun / Yaru Wang / Zheng Xing / Dongyu Li / Rong Wang / Baozhi Chen / Ning Zhou / Alyssa Ayala / Benjamin P Tu / Xiaofeng Qi /
Abstract: The Mitochondrial Pyruvate Carrier (MPC) bridges cytosolic and mitochondrial metabolism by transporting pyruvate into mitochondria for ATP production and biosynthesis of various essential molecules. ...The Mitochondrial Pyruvate Carrier (MPC) bridges cytosolic and mitochondrial metabolism by transporting pyruvate into mitochondria for ATP production and biosynthesis of various essential molecules. MPC functions as a heterodimer composed of MPC1 and MPC2 in most mammalian cells. Here, we present the cryogenic electron microscopy (cryo-EM) structures of the human MPC1-2 complex in the mitochondrial intermembrane space (IMS)-open state and the inhibitor-bound in the mitochondrial matrix-open state. Structural analysis shows that the transport channel of MPC is formed by the interaction of transmembrane helix (TM) 1 and TM2 of MPC1 with TM2 and TM1 of MPC2, respectively. UK5099, a potent MPC inhibitor, shares the same binding site with pyruvate at the matrix side of the transport channel, stabilizing MPC in its matrix-open conformation. Notably, a functional W82F mutation in MPC2 leads to the complex in an IMS-open conformation. Structural comparisons across different conformations, combined with yeast rescue assays, reveal the mechanisms of substrate binding and asymmetric conformational changes in MPC during pyruvate transport across the inner mitochondrial membrane (IMM) as well as the inhibitory mechanisms of MPC inhibitors.
History
DepositionApr 26, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70351.png

Downloads & links

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Map

FileDownload / File: emd_70351.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 340 pix.
= 250.92 Å		0.74 Å/pix.
x 340 pix.
= 250.92 Å		0.74 Å/pix.
x 340 pix.
= 250.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4325674 - 0.6894174
Average (Standard dev.)0.00012227175 (±0.009768011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 250.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70351_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_70351_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : MPC1-2

EntireName: MPC1-2
Components
  • Complex: MPC1-2
    • Protein or peptide: Human MPC1
    • Protein or peptide: Human MPC2

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Supramolecule #1: MPC1-2

SupramoleculeName: MPC1-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Human MPC1

MacromoleculeName: Human MPC1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGALVRKAA DYVRSKDFRD YLMSTHFWGP VANWGLPIAA INDMKKSPEI ISGRMTFALC CYSLTFMRFA YKVQPRNWLL FACHATNEVA QLIQGGRLIK HEMTKTASAG GGGSGGGGSG GGGSEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP ...String:
MAGALVRKAA DYVRSKDFRD YLMSTHFWGP VANWGLPIAA INDMKKSPEI ISGRMTFALC CYSLTFMRFA YKVQPRNWLL FACHATNEVA QLIQGGRLIK HEMTKTASAG GGGSGGGGSG GGGSEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW PLIAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLIDL IKNKHMNADT DYSIAEAAFN KGETAMTING PWAWSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EELVKDPRVA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD AALAAAQ

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Macromolecule #2: Human MPC2

MacromoleculeName: Human MPC2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAAGARGLR ATYHRLLDKV ELMLPEKLRP LYNHPAGPRT VFFWAPIMKW GLVCAGLADM ARPAEKLSTA QSAVLMATGF IFSRYSLVII PKNWSLFAVN FFVGAAGASQ LFRIWRYNQE LKAKDLGRKL LEAARAGQLD EVRILLANGA DVNAADNTGT TPLHLAAYSG ...String:
MSAAGARGLR ATYHRLLDKV ELMLPEKLRP LYNHPAGPRT VFFWAPIMKW GLVCAGLADM ARPAEKLSTA QSAVLMATGF IFSRYSLVII PKNWSLFAVN FFVGAAGASQ LFRIWRYNQE LKAKDLGRKL LEAARAGQLD EVRILLANGA DVNAADNTGT TPLHLAAYSG HLEIVEVLLK HGADVDASDV FGYTPLHLAA YWGHLEIVEV LLKNGADVNA MDSDGMTPLH LAAKWGYLEI VEVLLKHGAD VNAQDKFGKT AFDISIDNGN EDLAEILQKL N

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 382429
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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