9KNY: Mitochondrial pyruvate carrier 2

Cryo-EM structure of pyruvate-treated human mitochondrial pyruvate carrier in the IMS-open conformation at pH 8.0. Determined by electron microscopy at 3.4 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,747
Mol. weight: 47.98 kDa
Ligands: PC8, CDL
Released: 12 Mar 2025

Explore 9KNY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KNY contains 15 α-helices and 13 β-strands across 3 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	25-28	4
α-helix	32-34	3
α-helix	35-43	9
α-helix	48-50	3
α-helix	53-72	20
β-strand	74	1	1
α-helix	78-107	30

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	29-32	4
α-helix	41-56	16
α-helix	59-61	3
α-helix	64-66	3
α-helix	69-85	17
β-strand	90	1	1
α-helix	94-125	32

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	10-12	3	3
β-strand	17-25	9	2
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
β-strand	68-73	6	2
β-strand	78-84	7	2
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	104	1	3
β-strand	109-113	5	3

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 1	C	protein	138	Homo sapiens

Sequence of entity 1 (B), FASTA

>9KNY_1 Mitochondrial pyruvate carrier 2 (chains B)
MSAAGARGLRATYHRLLDKVELMLPEKLRPLYNHPAGPRTVFFWAPIMKWGLVCAGLADM
ARPAEKLSTAQSAVLMATGFIWSRYSLVIIPKNWSLFAVNFFVGAAGASQLFRIWRYNQE
LKAKAHKGSDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 2 (A), FASTA

>9KNY_2 Mitochondrial pyruvate carrier 1 (chains A)
MAGALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALC
CYSLTFMRFAYKVQPRNWLLFACHATNEVAQLIQGGRLIKHEMTKTASAGSYPYDVPDYA

Sequence of entity 3 (C), FASTA

>9KNY_3 MPC specific nanobody 1 (chains C)
EVQLVESGGGLVQAGGSLRLSCAASGFPVTERVMYWYRQAPGKEREWVAAIDSQGSSTYY
ADSVKGRFTISRDNSKNTVYLQMNSLKPEDTAVYYCKVEVGWGYKGQGTQVTVSSLEHHH
HHHHGGSGEQKLISEEDL

Ligands and cofactors

ID	Name	Formula	Copies
PC8	1,2-dioctanoyl-sn-glycero-3-phosphocholine	C24 H49 N O8 P	1
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
8YW9 3.01 Å, Cryo-EM structure of human mitochondrial pyruvate carrier in the matrix-facing…
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
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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