8ZUX | pdb_00008zux

Structure of G668R-hPCC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Nanoscale conformational dynamics of human propionyl-CoA carboxylase.

Yan, H.Ni, F.Wang, Q.Ma, J.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.10.009
  • Primary Citation of Related Structures:  
    8ZUX, 8ZUY, 8ZUZ, 8ZV0, 8ZV1, 8ZV2, 8ZV3, 8ZV4, 8ZV5, 8ZV6, 9UH1, 9UH2, 9UH5, 9UH6, 9UH8, 9UHB, 9UHR, 9UHS, 9UHY

  • PubMed Abstract: 

    Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic disorder driven by toxic metabolite accumulation. Despite its therapeutic relevance, the structural basis of hPCC's catalytic function remains unresolved. Here, we present high-resolution cryo-EM structures of hPCC in four distinct states, unliganded, ADP-, AMPPNP-, and ATP-bound/substrate-bound, capturing the full trajectory of the biotin carboxyl carrier protein (BCCP) domain as it translocates between active sites. Our results reinforce the crucial role of nucleotide-gated B-lid subdomain in synchronizing catalysis through coupling with BCCP movement. Structural and biochemical analysis of 10 disease-associated variants reveals how mutations disrupt key domain interfaces and dynamic motions required for activity. These new insights define the mechanistic principles governing hPCC functions, establish a structural framework for understanding PCC-related disorders, and lay the groundwork for future efforts to engineer functional replacements or modulators for metabolic therapy.


  • Organizational Affiliation
    • Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China; School of Life Sciences, Fudan University, Shanghai 200433, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Propionyl-CoA carboxylase alpha chain, mitochondrial728Homo sapiensMutation(s): 0 
Gene Names: PCCA
EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05165 (Homo sapiens)
Explore P05165 
Go to UniProtKB:  P05165
PHAROS:  P05165
GTEx:  ENSG00000175198 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05165
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Propionyl-CoA carboxylase beta chain, mitochondrial247Homo sapiensMutation(s): 0 
Gene Names: PCCB
EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05166 (Homo sapiens)
Explore P05166 
Go to UniProtKB:  P05166
PHAROS:  P05166
GTEx:  ENSG00000114054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05166
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Propionyl-CoA carboxylase beta chain, mitochondrialC [auth F]292Homo sapiensMutation(s): 0 
Gene Names: PCCB
EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05166 (Homo sapiens)
Explore P05166 
Go to UniProtKB:  P05166
PHAROS:  P05166
GTEx:  ENSG00000114054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05166
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2021YFF1200400
Other governmentChina2018SHZDZX01

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release