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- PDB-22fr: Structure of apo Cdr1 -

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Basic information

Entry
Database: PDB / ID: 22fr
TitleStructure of apo Cdr1
ComponentsPleiotropic ABC efflux transporter of multiple drugs CDR1
KeywordsMEMBRANE PROTEIN / Candida albicans / Multidrug resistance / Substrate efflux cycle
Function / homology
Function and homology information


fluconazole transmembrane transporter activity / fluconazole transport / azole transmembrane transporter activity / corticosterone binding / azole transmembrane transport / estradiol binding / aminophospholipid flippase activity / phosphatidylethanolamine floppase activity / phosphatidylserine floppase activity / phosphatidylcholine floppase activity ...fluconazole transmembrane transporter activity / fluconazole transport / azole transmembrane transporter activity / corticosterone binding / azole transmembrane transport / estradiol binding / aminophospholipid flippase activity / phosphatidylethanolamine floppase activity / phosphatidylserine floppase activity / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / phospholipid translocation / xenobiotic transmembrane transporter activity / ABC-type transporter activity / cellular response to xenobiotic stimulus / ribonucleoside triphosphate phosphatase activity / extracellular vesicle / nucleotide binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Pleiotropic drug resistance protein PDR/CDR / CDR ABC transporter / ABC-transporter, N-terminal domain / ATP-binding cassette transporter, PDR-like subfamily G, domain 1 / ATP-binding cassette transporter, PDR-like subfamily G, domain 2 / CDR ABC transporter / ABC-transporter N-terminal / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site ...Pleiotropic drug resistance protein PDR/CDR / CDR ABC transporter / ABC-transporter, N-terminal domain / ATP-binding cassette transporter, PDR-like subfamily G, domain 1 / ATP-binding cassette transporter, PDR-like subfamily G, domain 2 / CDR ABC transporter / ABC-transporter N-terminal / ABC-2 type transporter / ABC-2 type transporter / 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
Pleiotropic ABC efflux transporter of multiple drugs CDR1
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWang, Z. / Yang, S. / Zhang, B. / Yu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000896 China
CitationJournal: Sci Adv / Year: 2026
Title: Cryo-EM structures of Cdr1 reveal snapshots of substrate transport and diverse inhibitor recognition.
Authors: Zhen Wang / Shuting Yang / Binyu Zhang / Hengyi Jiang / Yinxia Li / Rongchao Gao / Yulong Wang / Fengying Fan / Lili Dong / Jiaxuan Qiu / Xiurui Li / Yue Zhou / Alastair I H Murchie / Xuekui Yu /
Abstract: In -a World Health Organization fungal priority pathogen-overexpression of the adenosine triphosphate (ATP)-binding cassette transporter Cdr1 drives multidrug resistance. We present seven cryo- ...In -a World Health Organization fungal priority pathogen-overexpression of the adenosine triphosphate (ATP)-binding cassette transporter Cdr1 drives multidrug resistance. We present seven cryo-electron microscopy structures capturing substrate entry and expulsion. An inward-facing transmembrane channel with three on-off substrate binding sites defines a proposed entry pathway for a single substrate molecule. Coordinated ATP binding to both nucleotide-binding domains induces transmembrane domain closure, driving the substrate expulsion; adenosine diphosphate release following ATP hydrolysis resets the transporter to an inward-open conformation, enabling substrate entry for the next translocation cycle. Structures with three structurally diverse inhibitors resolve two distinct binding modes: one occupying all three substrate sites and another specifically binding two extracellular-proximal sites. These findings provide snapshots of the substrate translocation cycle and structural blueprints for antifungal drug design.
History
DepositionJan 9, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleiotropic ABC efflux transporter of multiple drugs CDR1


Theoretical massNumber of molelcules
Total (without water)170,1601
Polymers170,1601
Non-polymers00
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 Pleiotropic ABC efflux transporter of multiple drugs CDR1 / Pleiotropic drug resistance protein CDR1


Mass: 170159.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: CDR1, CAALFM_C305220WA, CaO19.13421, CaO19.6000 / Production host: Homo sapiens (human) / References: UniProt: Q5ANA3
Has protein modificationY

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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: Apo Cdr1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Candida albicans SC5314 (yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 410230 / Symmetry type: POINT

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