8YW9: Mitochondrial pyruvate carrier 2

Cryo-EM structure of human mitochondrial pyruvate carrier in the matrix-facing conformation at pH 6.8. Determined by electron microscopy at 3.01 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Homo sapiens, Escherichia coli BL21(DE3)
Chains: 4
Atoms: 3,709
Mol. weight: 61.69 kDa
Ligands: CDL
Released: 12 Mar 2025

Explore 8YW9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YW9 contains 18 α-helices and 24 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	17-22	6
α-helix	25-33	9
α-helix	35-42	8
α-helix	43-45	3
α-helix	48-50	3
α-helix	53-72	20
α-helix	78-107	30

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	6-23	18
α-helix	29-32	4
α-helix	41-47	7
α-helix	50-58	9
α-helix	59-61	3
α-helix	69-88	20
α-helix	94-125	32

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-13	4	2
β-strand	17-25	9	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	102-104	3	3
β-strand	107-109	3	3
β-strand	116-117	2	2
β-strand	121-126	6	2

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-12	3	5
β-strand	18-25	8	4
β-strand	34-39	6	5
β-strand	46-51	6	5
β-strand	58-60	3	5
α-helix	62-64	3
β-strand	68-73	6	4
α-helix	74-76	3
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-98	7	5
β-strand	104-105	2	5
β-strand	109-113	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial pyruvate carrier 2	B	protein	151	Homo sapiens	O95563 (AlphaFold model)
Mitochondrial pyruvate carrier 1	A	protein	120	Homo sapiens	Q9Y5U8 (AlphaFold model)
MPC specific nanobody 2	C	protein	127	Escherichia coli BL21(DE3)
MPC specific nanobody 1	D	protein	138	Escherichia coli BL21(DE3)

Sequence of entity 1 (B), FASTA

>8YW9_1 Mitochondrial pyruvate carrier 2 (chains B)
MSAAGARGLRATYHRLLDKVELMLPEKLRPLYNHPAGPRTVFFWAPIMKWGLVCAGLADM
ARPAEKLSTAQSAVLMATGFIWSRYSLVIIPKNWSLFAVNFFVGAAGASQLFRIWRYNQE
LKAKAHKGSDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 2 (A), FASTA

>8YW9_2 Mitochondrial pyruvate carrier 1 (chains A)
MAGALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALC
CYSLTFMRFAYKVQPRNWLLFACHATNEVAQLIQGGRLIKHEMTKTASAGSYPYDVPDYA

Sequence of entity 3 (C), FASTA

>8YW9_3 MPC specific nanobody 2 (chains C)
EVQLVESGGGLVQAGGSLRLSCAASGITYRHYAIGWFRQAPGKEREGVARIRSSTGQTYY
ADSVKGRFTMSRDNSKNTVYLQMNSLKPEDTALYYCAYGPLYYYEGGWAWPNYYDYWGQG
TQVTVSS

Sequence of entity 4 (D), FASTA

>8YW9_4 MPC specific nanobody 1 (chains D)
EVQLVESGGGLVQAGGSLRLSCAASGFPVTERVMYWYRQAPGKEREWVAAIDSQGSSTYY
ADSVKGRFTISRDNSKNTVYLQMNSLKPEDTAVYYCKVEVGWGYKGQGTQVTVSSLEHHH
HHHHGGSGEQKLISEEDL

Ligands and cofactors

ID	Name	Formula	Copies
CDL	Cardiolipin	C81 H156 O17 P2	1

Primary citation

Structures and mechanism of the human mitochondrial pyruvate carrier. Liang, J., Shi, J., Song, A. et al. Nature (2025) 641:258-265. DOI 10.1038/s41586-025-08873-8 · PubMed

Other PDB entries of the same protein (UniProt O95563 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MNZ 2.73 Å, Cryo-EM structure of human MPC in complex with UK5099 in nanodiscs
9MNY 2.78 Å, Cryo-EM structure of human MPC with pyruvate
9MO0 2.83 Å, Cryo-EM structure of human MPC in complex with AKOS005153046
9MNX 3.11 Å, Cryo-EM structure of human MPC in complex with UK5099 in LMNG
8YW8 3.17 Å, Cryo-EM structure of human mitochondrial pyruvate carrier in complex with the inhibitor…
8YW6 3.18 Å, Cryo-EM structure of apo human mitochondrial pyruvate carrier in the IMS-open…
9O9T 3.31 Å, Structure of human MPC IMS-open
9MNW 3.35 Å, Cryo-EM structure of human MPC in complex with GW604714
9KNY 3.4 Å, Cryo-EM structure of pyruvate-treated human mitochondrial pyruvate carrier in the…
9KNW 3.41 Å, Cryo-EM structure of apo human mitochondrial pyruvate carrier in the IMS-open…
9O9S 3.57 Å, Structure of human MPC matrix-open
9GIV 3.65 Å, Structure of the human mitochondrial pyruvate carrier inhibited by a UK5099-derivative

Browse structure collections

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