8YW9

Cryo-EM structure of human mitochondrial pyruvate carrier in the matrix-facing conformation at pH 6.8

• PDB DOI: https://doi.org/10.2210/pdb8YW9/pdb
• EM Map EMD-39626: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens, Escherichia coli BL21(DE3)
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-30 Released: 2025-03-12 
• Deposition Author(s): Shi, J.H., Liang, J.M., Ma, D.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A membrane transporter complex with substrate

Shi, J.H., Liang, J.M., Ma, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 61.69 kDa 
• Atom Count: 3,709 
• Modelled Residue Count: 458 
• Deposited Residue Count: 536 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial pyruvate carrier 2	A [auth B]	151	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial pyruvate carrier 1	B [auth A]	120	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MPC specific nanobody 2	C	127	Escherichia coli BL21(DE3)	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MPC specific nanobody 1	D	138	Escherichia coli BL21(DE3)	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	E [auth B]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1_3660:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Shi, J.H., Liang, J.M., Ma, D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFA1303700

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release