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- EMDB-70262: Structure of human MPC IMS-open -

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Basic information

Entry
Database: EMDB / ID: EMD-70262
TitleStructure of human MPC IMS-open
Map data
Sample
  • Complex: MPC1-2
    • Protein or peptide: Mitochondrial pyruvate carrier 2
    • Protein or peptide: Mitochondrial pyruvate carrier 1/MBP chimera protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


pyruvate import into mitochondria / inner mitochondrial membrane protein complex / pyruvate transmembrane transporter activity / pyruvate decarboxylation to acetyl-CoA / Pyruvate metabolism / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...pyruvate import into mitochondria / inner mitochondrial membrane protein complex / pyruvate transmembrane transporter activity / pyruvate decarboxylation to acetyl-CoA / Pyruvate metabolism / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / mitochondrial inner membrane / DNA damage response / mitochondrion / identical protein binding / membrane / nucleus
Similarity search - Function
Mitochondrial pyruvate carrier / Mitochondrial pyruvate carriers / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Mitochondrial pyruvate carrier 2 / Maltose/maltodextrin-binding periplasmic protein / Mitochondrial pyruvate carrier 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli K-12 (bacteria)
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 18, 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_70262.png

Downloads & links

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Map

FileDownload / File: emd_70262.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
AxesX (Sec.)Y (Row.)Z (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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum-44.580739999999999 - 59.027386
Average (Standard dev.)-0.030044032 (±0.90450865)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : MPC1-2

EntireName: MPC1-2
Components
  • Complex: MPC1-2
    • Protein or peptide: Mitochondrial pyruvate carrier 2
    • Protein or peptide: Mitochondrial pyruvate carrier 1/MBP chimera protein

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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: Mitochondrial pyruvate carrier 2

MacromoleculeName: Mitochondrial pyruvate carrier 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.786404 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAAGARGLR ATYHRLLDKV ELMLPEKLRP LYNHPAGPRT VFFWAPIMKW GLVCAGLADM ARPAEKLSTA QSAVLMATGF IFSRYSLVI IPKNWSLFAV NFFVGAAGAS QLFRIWRYNQ ELKAKDLGRK LLEAARAGQL DEVRILLANG ADVNAADNTG T TPLHLAAY ...String:
MSAAGARGLR ATYHRLLDKV ELMLPEKLRP LYNHPAGPRT VFFWAPIMKW GLVCAGLADM ARPAEKLSTA QSAVLMATGF IFSRYSLVI IPKNWSLFAV NFFVGAAGAS QLFRIWRYNQ ELKAKDLGRK LLEAARAGQL DEVRILLANG ADVNAADNTG T TPLHLAAY SGHLEIVEVL LKHGADVDAS DVFGYTPLHL AAYWGHLEIV EVLLKNGADV NAMDSDGMTP LHLAAKWGYL EI VEVLLKH GADVNAQDKF GKTAFDISID NGNEDLAEIL QKLN

UniProtKB: Mitochondrial pyruvate carrier 2

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Macromolecule #2: Mitochondrial pyruvate carrier 1/MBP chimera protein

MacromoleculeName: Mitochondrial pyruvate carrier 1/MBP chimera protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 53.069273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGALVRKAA DYVRSKDFRD YLMSTHFWGP VANWGLPIAA INDMKKSPEI ISGRMTFALC CYSLTFMRFA YKVQPRNWLL FACHATNEV AQLIQGGRLI KHEMTKTASA GGGGSGGGGS GGGGSEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV E HPDKLEEK ...String:
MAGALVRKAA DYVRSKDFRD YLMSTHFWGP VANWGLPIAA INDMKKSPEI ISGRMTFALC CYSLTFMRFA YKVQPRNWLL FACHATNEV AQLIQGGRLI KHEMTKTASA GGGGSGGGGS GGGGSEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV E HPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YN KDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL IDL IKNKHM NADTDYSIAE AAFNKGETAM TINGPWAWSN IDTSKVNYGV TVLPTFKGQP SKPFVGVLSA GINAASPNKE LAKE FLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELVK DPRVAATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTVD AALA AAQ

UniProtKB: Mitochondrial pyruvate carrier 1, Maltose/maltodextrin-binding periplasmic protein

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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: 382439
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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