9O9S: Human MPC matrix-open

Structure of human MPC matrix-open. Determined by electron microscopy at 3.57 Å resolution. Released 30 Jul 2025.

Method: Electron microscopy
Resolution: 3.57 Å
Organisms: Homo sapiens, Escherichia coli K-12
Chains: 2
Atoms: 5,322
Mol. weight: 84.18 kDa
Ligands: I2R
Released: 30 Jul 2025

Explore 9O9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O9S contains 39 α-helices and 25 β-strands across 2 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: 27 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	25-42	18
α-helix	48-50	3
α-helix	53-71	19
α-helix	78-102	25
β-strand	128-132	5	1
α-helix	139-152	14
β-strand	156-160	5	1
α-helix	165-173	9
β-strand	181-185	5	1
α-helix	186-188	3
α-helix	189-194	6
β-strand	198	1	2
α-helix	199-201	3
α-helix	205-210	6
β-strand	211	1	3
α-helix	213-218	6
β-strand	220-221	2	4
β-strand	224-225	2	4
β-strand	228-233	6	1
β-strand	236-240	5	5
β-strand	250	1	6
α-helix	253-262	10
α-helix	276-286	11
β-strand	293	1	7
β-strand	298	1	7
α-helix	304-306	3
α-helix	308-322	15
α-helix	332-340	9
β-strand	346-349	4	5
α-helix	351-353	3
α-helix	354-359	6
β-strand	364-367	4	5
α-helix	368-370	3
β-strand	371	1	6
β-strand	372	1	8
β-strand	375	1	8
α-helix	376-377	2
β-strand	380-381	2	9
β-strand	382-388	7	1
β-strand	389	1	2
α-helix	395-400	6
α-helix	401-406	6
α-helix	409-418	10
β-strand	423-424	2	1
β-strand	426	1	3
α-helix	427-433	7
α-helix	437-448	12
β-strand	450-451	2	9
α-helix	458-473	16
α-helix	479-486	8

Chain B: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	44-61	18
α-helix	69-86	18
α-helix	96-136	41
α-helix	139-147	9
α-helix	162-169	8
α-helix	172-180	9
α-helix	195-201	7
α-helix	205-213	9
α-helix	228-235	8
α-helix	238-246	9
β-strand	254	1	10
β-strand	260	1	10
α-helix	261-267	7
α-helix	271-280	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial pyruvate carrier 1/MBP chimera protein	A	protein	487	Homo sapiens, Escherichia coli K-12	Q9Y5U8 (AlphaFold model)
Mitochondrial pyruvate carrier 2	B	protein	281	Homo sapiens	O95563 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9O9S_1 Mitochondrial pyruvate carrier 1/MBP chimera protein (chains A)
MAGALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALC
CYSLTFMRFAYKVQPRNWLLFACHATNEVAQLIQGGRLIKHEMTKTASAGGGGSGGGGSG
GGGSEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPD
IIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYN
KDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDI
KDVGVDNAGAKAGLTFLIDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTS
KVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKP
LGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVD
AALAAAQ

Sequence of entity 2 (B), FASTA

>9O9S_2 Mitochondrial pyruvate carrier 2 (chains B)
MSAAGARGLRATYHRLLDKVELMLPEKLRPLYNHPAGPRTVFFWAPIMKWGLVCAGLADM
ARPAEKLSTAQSAVLMATGFIWSRYSLVIIPKNWSLFAVNFFVGAAGASQLFRIWRYNQE
LKAKDLGRKLLEAARAGQLDEVRILLANGADVNAADNTGTTPLHLAAYSGHLEIVEVLLK
HGADVDASDVFGYTPLHLAAYWGHLEIVEVLLKNGADVNAMDSDGMTPLHLAAKWGYLEI
VEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
I2R	(E)-2-cyano-3-(1-phenylindol-3-yl)prop-2-enoic acid	C18 H12 N2 O2	1

Primary citation

Structure of human mitochondrial pyruvate carrier MPC1 and MPC2 complex. Sun, Y., Wang, Y., Xing, Z. et al. Nat Commun (2025) 16:6700-6700. DOI 10.1038/s41467-025-61939-z · 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
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
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…
9KNX 3.72 Å, Cryo-EM structure of human mitochondrial pyruvate carrier in the occluded conformation…

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