9XSM | pdb_00009xsm

CydDC in nanodisc with heme-bound I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XSM

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Literature

Conformational Snapshots of CydDC in a Native Lipid Bilayer Coupling Heme Transport to Antibiotic Resistance.

Yang, L.Zhang, C.Lyu, M.Luo, Y.Zhang, J.Chen, Y.Luo, L.Qiao, W.Li, X.Zhou, Y.Wei, Z.Xiao, Y.Niu, Q.Zhou, J.He, G.Ying, B.Su, Z.Chen, H.Tang, X.Dong, H.

(2026) Adv Sci (Weinh) : e76081-e76081

  • DOI: https://doi.org/10.1002/advs.76081
  • Primary Citation Related Structures: 
    9TBY, 9XNO, 9XNP, 9XSM, 9XUO

  • PubMed Abstract: 

    Heme is an essential cofactor in numerous biological processes, including bacterial respiration. The ABC transporter CydDC facilitates the assembly and maturation of the cytochrome bd terminal oxidase by exporting heme and has been implicated in antibiotic resistance in bacteria. However, the dynamic conformations of CydDC in a native-like lipid bilayer remain unresolved, and its resistance mechanism is still elusive. Here, we determined high-resolution cryo-electron microscopy structures of nanodisc-reconstituted CydDC in the apo, nucleotide-bound and heme-bound states, providing direct structural evidence for its substrate-stimulated hydrolysis mechanism. In vivo and in vitro biochemical characterization identified key residues of CydDC that are critical for substrate binding and transport. Bioinformatics analysis further demonstrated that CydDC is highly conserved across bacterial species. Transcriptomic profiling of cydC/D in antibiotic-resistant strains showed that elevated expression of cydC/D correlates with increased antibiotic resistance. Moreover, mutations at the heme-binding sites altered bacterial susceptibility to multiple antibiotics, suggesting that the exporting activity of CydDC may also contribute directly to drug resistance. Together, these findings provide mechanistic insights into CydDC-mediated heme transport and potential drug efflux, and inform the development of antimicrobial strategies targeting the respiratory chain.


  • Organizational Affiliation
    • Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.

Macromolecule Content 

  • Total Structure Weight: 130.05 kDa 
  • Atom Count: 8,977 
  • Modeled Residue Count: 1,154 
  • Deposited Residue Count: 1,172 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione/L-cysteine transport system ATP-binding/permease protein CydCA [auth C]584Escherichia coli K-12Mutation(s): 0 
Gene Names: cydCmdrAmdrHsurBb0886JW0869
EC: 7.4.2
UniProt
Find proteins for P23886 (Escherichia coli (strain K12))
Explore P23886 
Go to UniProtKB:  P23886
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23886
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione/L-cysteine transport system ATP-binding/permease protein CydDB [auth D]588Escherichia coli K-12Mutation(s): 0 
Gene Names: cydDhtrDb0887JW0870
EC: 7.4.2
UniProt
Find proteins for P29018 (Escherichia coli (strain K12))
Explore P29018 
Go to UniProtKB:  P29018
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29018
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
C [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15.2_3472
RECONSTRUCTIONPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release