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- EMDB-67054: CydDC in nanodisc with AMP-PNP-bound -

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Basic information

Entry
Database: EMDB / ID: EMD-67054
TitleCydDC in nanodisc with AMP-PNP-bound
Map data
Sample
  • Complex: CydDC in nanodisc
    • Protein or peptide: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC
    • Protein or peptide: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsAMP-PNP bound / TRANSPORT PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZhang C / Luo Y / Yang L
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67054.png

Downloads & links

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Map

FileDownload / File: emd_67054.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 352 pix.
= 299.2 Å		0.85 Å/pix.
x 352 pix.
= 299.2 Å		0.85 Å/pix.
x 352 pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.251
Minimum - Maximum-0.7878483 - 1.505511
Average (Standard dev.)0.0011470998 (±0.030914094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67054_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67054_half_map_2.map
Projections & Slices
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Sample components

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Entire : CydDC in nanodisc

EntireName: CydDC in nanodisc
Components
  • Complex: CydDC in nanodisc
    • Protein or peptide: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC
    • Protein or peptide: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: CydDC in nanodisc

SupramoleculeName: CydDC in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Glutathione/L-cysteine transport system ATP-binding/permease prot...

MacromoleculeName: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 64.317254 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGAA ITRTAGRYFE RLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL LNRVVADVDT LDHLYLRVIS PLVGAFVVIM VVTIGLSFLD F TLAFTLGG ...String:
MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGAA ITRTAGRYFE RLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL LNRVVADVDT LDHLYLRVIS PLVGAFVVIM VVTIGLSFLD F TLAFTLGG IMLLTLFLMP PLFYRAGKST GQNLTHLRGQ YRQQLTAWLQ GQAELTIFGA SDRYRTQLEN TEIQWLEAQR RQ SELTALS QAIMLLIGAL AVILMLWMAS GGVGGNAQPG ALIALFVFCA LAAFEALAPV TGAFQHLGQV IASAVRISDL TDQ KPEVTF PDTQTRVADR VSLTLRDVQF TYPEQSQQAL KGISLQVNAG EHIAILGRTG CGKSTLLQQL TRAWDPQQGE ILLN DSPIA SLNEAALRQT ISVVPQRVHL FSATLRDNLL LASPGSSDEA LSEILRRVGL EKLLEDAGLN SWLGEGGRQL SGGEL RRLA IARALLHDAP LVLLDEPTEG LDATTESQIL ELLAEMMREK TVLMVTHRLR GLSRFQQIIV MDNGQIIEQG THAELL ARQ GRYYQFKQGL GSSHHHHHHH H

UniProtKB: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC

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Macromolecule #2: Glutathione/L-cysteine transport system ATP-binding/permease prot...

MacromoleculeName: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 65.118867 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLLV LTFVLRAWVV WLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA GSWATLVLEQ IDDMHDYYAR YLPQMALAVS VPLLIVVAIF P SNWAAALI ...String:
MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLLV LTFVLRAWVV WLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA GSWATLVLEQ IDDMHDYYAR YLPQMALAVS VPLLIVVAIF P SNWAAALI LLGTAPLIPL FMALVGMGAA DANRRNFLAL ARLSGHFLDR LRGMETLRIF GRGEAEIESI RSASEDFRQR TM EVLRLAF LSSGILEFFT SLSIALVAVY FGFSYLGELD FGHYDTGVTL AAGFLALILA PEFFQPLRDL GTFYHAKAQA VGA ADSLKT FMETPLAHPQ RGEAELASTD PVTIEAEELF ITSPEGKTLA GPLNFTLPAG QRAVLVGRSG SGKSSLLNAL SGFL SYQGS LRINGIELRD LSPESWRKHL SWVGQNPQLP AATLRDNVLL ARPDASEQEL QAALDNAWVS EFLPLLPQGV DTPVG DQAA RLSVGQAQRV AVARALLNPC SLLLLDEPAA SLDAHSEQRV MEALNAASLR QTTLMVTHQL EDLADWDVIW VMQDGR IIE QGRYAELSVA GGPFATLLAH RQEEI

UniProtKB: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.21)
Software - details: PHENIX1.21 was used to refine the final model
Number images used: 424631
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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