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- EMDB-70261: Structure of human MPC matrix-open -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70261
TitleStructure of human MPC matrix-open
Map data
Sample
  • Complex: MPC1-2
    • Protein or peptide: Mitochondrial pyruvate carrier 1/MBP chimera protein
    • Protein or peptide: Mitochondrial pyruvate carrier 2
  • Ligand: (E)-2-cyano-3-(1-phenylindol-3-yl)prop-2-enoic acid
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 / nucleus / membrane
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: 3.57 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: To Be Published
Title: Structure of human MPC matrix-open
Authors: Qi X / Sun Y / Wang Y
History
DepositionApr 18, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70261.png

Downloads & links

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Map

FileDownload / File: emd_70261.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: 7.5
Minimum - Maximum-33.509369999999997 - 57.585728000000003
Average (Standard dev.)0.0028956176 (±0.9621863)
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 1/MBP chimera protein
    • Protein or peptide: Mitochondrial pyruvate carrier 2
  • Ligand: (E)-2-cyano-3-(1-phenylindol-3-yl)prop-2-enoic acid

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Supramolecule #1: MPC1-2

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

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

MacromoleculeName: Mitochondrial pyruvate carrier 1/MBP chimera protein / type: protein_or_peptide / ID: 1 / 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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Macromolecule #2: Mitochondrial pyruvate carrier 2

MacromoleculeName: Mitochondrial pyruvate carrier 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.825439 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAAGARGLR ATYHRLLDKV ELMLPEKLRP LYNHPAGPRT VFFWAPIMKW GLVCAGLADM ARPAEKLSTA QSAVLMATGF IWSRYSLVI IPKNWSLFAV NFFVGAAGAS QLFRIWRYNQ ELKAKDLGRK LLEAARAGQL DEVRILLANG ADVNAADNTG T TPLHLAAY ...String:
MSAAGARGLR ATYHRLLDKV ELMLPEKLRP LYNHPAGPRT VFFWAPIMKW GLVCAGLADM ARPAEKLSTA QSAVLMATGF IWSRYSLVI 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 #3: (E)-2-cyano-3-(1-phenylindol-3-yl)prop-2-enoic acid

MacromoleculeName: (E)-2-cyano-3-(1-phenylindol-3-yl)prop-2-enoic acid / type: ligand / ID: 3 / Number of copies: 1 / Formula: I2R
Molecular weightTheoretical: 288.3 Da
Chemical component information

ChemComp-I2R:
(E)-2-cyano-3-(1-phenylindol-3-yl)prop-2-enoic acid

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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: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 197151
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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