9MNW

Cryo-EM structure of human MPC in complex with GW604714

• PDB DOI: https://doi.org/10.2210/pdb9MNW/pdb
• EM Map EMD-48441: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN/IMMUNE SYSTEM/INHIBITOR
• Organism(s): Homo sapiens, Mus musculus, synthetic construct, Escherichia coli
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-24 Released: 2025-03-05 
• Deposition Author(s): Zhang, J., Feng, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Stanford University

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of mitochondrial pyruvate carrier and its inhibition mechanism

He, Z., Zhang, J., Xu, Y., Fine, E.J., Suomivuori, C.M., Dror, R.O., Feng, L.

(2025) Nature 

• DOI: https://doi.org/10.1038/s41586-025-08667-y

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 159.98 kDa 
• Atom Count: 4,870 
• Modelled Residue Count: 614 
• Deposited Residue Count: 1,451 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial pyruvate carrier 1	A	115	Homo sapiens	Mutation(s): 0  Gene Names: MPC1, BRP44L, CGI-129, HSPC040, PNAS-115
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5U8 (Homo sapiens) Explore Q9Y5U8  Go to UniProtKB:  Q9Y5U8
PHAROS:  Q9Y5U8 GTEx:  ENSG00000060762

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial pyruvate carrier 2	B	127	Homo sapiens	Mutation(s): 0  Gene Names: MPC2, BRP44
UniProt & NIH Common Fund Data Resources
Find proteins for O95563 (Homo sapiens) Explore O95563  Go to UniProtKB:  O95563
PHAROS:  O95563 GTEx:  ENSG00000143158

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab_8D3_2 heavy chain	C [auth D]	265	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab_8D3_2 light chain	D [auth E]	247	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	E [auth C]	152	synthetic construct	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
MBP-PrA/G	F	545	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BM8 (Subject of Investigation/LOI)	G [auth B]	(5E)-5-({(5P)-5-[6-(4-acetylpiperazin-1-yl)-3-nitropyridin-2-yl]-2-fluorophenyl}methylidene)-1,3-thiazolidine-2,4-dione C21 H18 F N5 O5 S WZGVKWZJGXGNDP-GZTJUZNOSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Zhang, J., Feng, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
Stanford University	United States	--

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release