9MNY: Human MPC with pyruvate

Cryo-EM structure of human MPC with pyruvate. Determined by electron microscopy at 2.78 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.78 Å
Organisms: Homo sapiens, Mus musculus, synthetic construct
Chains: 6
Atoms: 5,332
Mol. weight: 159.69 kDa
Ligands: PYR
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9MNY contains 25 α-helices and 41 β-strands across 6 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	9-13	5
α-helix	16-23	8
α-helix	25-33	9
α-helix	35-43	9
α-helix	48-50	3
α-helix	53-72	20
α-helix	78-111	34
α-helix	113-114	2

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	25-27	3
α-helix	41-57	17
α-helix	64-66	3
α-helix	69-88	20
α-helix	94-122	29

Chain C: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	7
β-strand	7	1	8
β-strand	10-13	4	9
β-strand	18-20	3	10
β-strand	21	1	8
β-strand	23	1	10
β-strand	24-26	3	7
β-strand	30-39	10	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	64	1	10
β-strand	67-72	6	10
β-strand	77-82	6	10
α-helix	87-89	3
β-strand	91-100	10	9
β-strand	105-108	4	9
β-strand	112-117	6	9

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
β-strand	33-39	7	3
β-strand	45-51	7	3
β-strand	58-60	3	3
β-strand	65	1	1
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-84	7	1
β-strand	92-99	8	3
β-strand	118-119	2	3
β-strand	120-121	2	2

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	4
β-strand	10-11	2	5
β-strand	19-25	7	4
β-strand	30-31	2	6
β-strand	36-37	2	6
β-strand	39-44	6	5
β-strand	51-55	5	5
β-strand	59-60	2	5
α-helix	61	1
β-strand	68-72	5	4
β-strand	76-81	6	4
β-strand	91-96	6	5
β-strand	102-103	2	5
β-strand	107-109	3	5

Chain F: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	364-369	6
α-helix	375-386	12
α-helix	392-405	14
α-helix	421-428	8
α-helix	435-447	13
α-helix	449-451	3
α-helix	452-463	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial pyruvate carrier 1	A	protein	115	Homo sapiens	Q9Y5U8 (AlphaFold model)
Mitochondrial pyruvate carrier 2	B	protein	127	Homo sapiens	O95563 (AlphaFold model)
Fab_8D3_2 heavy chain	D	protein	265	Mus musculus
Fab_8D3_2 light chain	E	protein	247	Mus musculus
Nanobody	C	protein	152	synthetic construct
Mbp-pra/g	F	protein	545	Escherichia coli

Sequence of entity 1 (A), FASTA

>9MNY_1 Mitochondrial pyruvate carrier 1 (chains A)
MAGALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALC
CYSLTFMRFAYKVQPRNWLLFACHATNEVAQLIQGGRLIKHEMTKTASALEVLFQ

Sequence of entity 2 (B), FASTA

>9MNY_2 Mitochondrial pyruvate carrier 2 (chains B)
MSAAGARGLRATYHRLLDKVELMLPEKLRPLYNHPAGPRTVFFWAPIMKWGLVCAGLADM
ARPAEKLSTAQSAWLMATGFIWSRYSLVIIPKNWSLFAVNFFVGAAGASQLFRIWRYNQE
LKAKAHK

Sequence of entity 3 (D), FASTA

>9MNY_3 Fab_8D3_2 heavy chain (chains D)
MDWTWRVFCLLAVAPGAHSDVQLVESGGGLVQPGKSLRLSCAASGFTFSNFGMHWVRQAP
EMGLEWVAYISSGSTTKYYGDTVKGRFTISRDNPKNTLYLQMNSLRSEDTAMYYCARRPL
YDGDYGYPMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV
EPKSCGSLEVLFQGPHHHHHHHHHH

Sequence of entity 4 (E), FASTA

>9MNY_4 Fab_8D3_2 light chain (chains E)
MVLQTQVFISLLLWISGAYGNIMLTQSPSSLAVSAGERVTMSCKSTQSILYNSNQKTYLA
WYQQKPGQSPKLLIYWASTRASGVPDRFTGSGSGTDFTLTINSVQPEDLAVYYCHQYLSA
WTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQ
SGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECW
SHPQFEK

Sequence of entity 5 (C), FASTA

>9MNY_5 Nanobody (chains C)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQAGGSLRLSCAASGTIFYYGTMGWYR
QAPGKERELVASINRGGNTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVK
SGLIYAHRYWGQGTQVTVSSLEHHHHHHHHHH

Sequence of entity 6 (F), FASTA

>9MNY_6 MBP-PrA/G (chains F)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDQ
ALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNEHQAPKGGSGGAGSGDQ
QSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAGGGSGGGSGGSAV
TTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEGSGH
HHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PYR	Pyruvic acid	C3 H4 O3	1

Primary citation

Structure of mitochondrial pyruvate carrier and its inhibition mechanism. He, Z., Zhang, J., Xu, Y. et al. Nature (2025) 641:250-257. DOI 10.1038/s41586-025-08667-y · PubMed

Other PDB entries of the same protein (UniProt Q9Y5U8 (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
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
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
9KNX 3.72 Å, Cryo-EM structure of human mitochondrial pyruvate carrier in the occluded conformation…

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