9KNW | pdb_00009knw

Cryo-EM structure of apo human mitochondrial pyruvate carrier in the IMS-open conformation at pH 6.8

• PDB DOI: https://doi.org/10.2210/pdb9KNW/pdb
• EM Map EMD-62464: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-11-19 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: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A membrane transporter complex

Shi, J.H., Liang, J.M., Ma, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 47.98 kDa 
• Atom Count: 2,747 
• Modelled Residue Count: 333 
• Deposited Residue Count: 409 
• Unique protein chains: 3

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 Membrane Entity: Yes
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 Membrane Entity: Yes
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 1	C	138	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	D [auth B]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC8	E [auth A]	1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C24 H49 N O8 P YHIXRNNWDBPKPW-JOCHJYFZSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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