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- PDB-9xno: CydDC in nanodisc with AMP-PNP-bound -

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Basic information

Entry
Database: PDB / ID: 9xno
TitleCydDC in nanodisc with AMP-PNP-bound
Components
  • Glutathione/L-cysteine transport system ATP-binding/permease protein CydC
  • Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
KeywordsTRANSPORT PROTEIN / AMP-PNP bound
Function / homology
Function and homology information


L-cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / ABC-type heme transporter activity / heme transmembrane transport / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / glutathione transmembrane transport / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cell redox homeostasis ...L-cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / ABC-type heme transporter activity / heme transmembrane transport / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / glutathione transmembrane transport / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cell redox homeostasis / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC / ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Glutathione/L-cysteine transport system ATP-binding/permease protein CydC / Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZhang, C. / Luo, Y. / Yang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Sci (Weinh) / Year: 2026
Title: Conformational Snapshots of CydDC in a Native Lipid Bilayer Coupling Heme Transport to Antibiotic Resistance.
Authors: Lili Yang / Changbin Zhang / Mengyuan Lyu / Yongbo Luo / Jierou Zhang / Yujiao Chen / Lintao Luo / Wen Qiao / Xiangyangpeng Li / Yu Zhou / Zhongling Wei / Yuling Xiao / Qian Niu / Juan Zhou ...Authors: Lili Yang / Changbin Zhang / Mengyuan Lyu / Yongbo Luo / Jierou Zhang / Yujiao Chen / Lintao Luo / Wen Qiao / Xiangyangpeng Li / Yu Zhou / Zhongling Wei / Yuling Xiao / Qian Niu / Juan Zhou / Guanglin He / Binwu Ying / Zhaoming Su / Hao Chen / Xiaodi Tang / Haohao Dong /
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 ...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.
History
DepositionNov 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC
D: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4976
Polymers129,4362
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutathione/L-cysteine transport system ATP-binding/permease protein CydC


Mass: 64317.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: cydC, mdrA, mdrH, surB, b0886, JW0869 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P23886, Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
#2: Protein Glutathione/L-cysteine transport system ATP-binding/permease protein CydD


Mass: 65118.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: cydD, htrD, b0887, JW0870 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P29018, Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CydDC in nanodisc / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: 83333 (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 66.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1EMAN2.31particle selectionEMAN2.31 was used to automatically select particle images
9PHENIX1.15.2_3472model refinement
13PHENIX1.213D reconstructionPHENIX1.21 was used to refine the final model
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 424631 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089175
ELECTRON MICROSCOPYf_angle_d0.76612480
ELECTRON MICROSCOPYf_dihedral_angle_d14.0645447
ELECTRON MICROSCOPYf_chiral_restr0.0491449
ELECTRON MICROSCOPYf_plane_restr0.0051589

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