8X03 | pdb_00008x03

Structure of mitochondrial soluble protein

• PDB DOI: https://doi.org/10.2210/pdb8X03/pdb
• EM Map EMD-37969: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2023-11-03 Released: 2024-11-06 
• Deposition Author(s): Zhang, S.S., Chen, M.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular architecture of mammalian pyruvate dehydrogenase complex.

Chen, M., Song, Y., Zhang, S., Zhang, Y., Chen, X., Zhang, M., Han, M., Gao, X., Li, S., Yang, M.

(2025) Protein Cell 16: 72-78

• PubMed: 39180277 
• DOI: https://doi.org/10.1093/procel/pwae044
• Primary Citation Related Structures: 
  8X03

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Organizational Affiliation: 
• Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.
State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China.
Protein Research Technology Center, Protein Chemistry and Omics Platform, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia China.
Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen 518055, China.
Beijing Life Science Academy, Beijing 102209, China.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 4,155.75 kDa 
• Atom Count: 105,540 
• Modeled Residue Count: 13,740 
• Deposited Residue Count: 38,820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase component of pyruvate dehydrogenase complex	A, AA [auth a], AB [auth 0], B, BA [auth b], BB [auth 1], C, CA [auth c], CB [auth 2], D, DA [auth d], DB [auth 3], E, EA [auth e], EB [auth 4], F, FA [auth f], FB [auth 5], G, GA [auth g], GB [auth 6], H, HA [auth h], HB [auth 7], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	647	Sus scrofa	Mutation(s): 0  EC: 2.3.1.12
UniProt
Find proteins for A0A4X1TBD2 (Sus scrofa) Explore A0A4X1TBD2  Go to UniProtKB:  A0A4X1TBD2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Zhang, S.S., Chen, M.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21532004, 31570733

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 1.1: 2025-01-15
  Changes: Data collection, Database references