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- EMDB-68246: Structure of apo Cdr1 -

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Basic information

Entry
Database: EMDB / ID: EMD-68246
TitleStructure of apo Cdr1
Map dataNone
Sample
  • Complex: Apo Cdr1
    • Protein or peptide: Pleiotropic ABC efflux transporter of multiple drugs CDR1
KeywordsCandida albicans / Multidrug resistance / Substrate efflux cycle / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWang Z / Yang S / Zhang B / Yu X
Funding support China, 1 items
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, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68246.png

Downloads & links

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Map

FileDownload / File: emd_68246.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318.3 Å		1.06 Å/pix.
x 300 pix.
= 318.3 Å		1.06 Å/pix.
x 300 pix.
= 318.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.6329144 - 3.2385337
Average (Standard dev.)-0.015335318 (±0.0763316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: None

Fileemd_68246_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68246_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Apo Cdr1

EntireName: Apo Cdr1
Components
  • Complex: Apo Cdr1
    • Protein or peptide: Pleiotropic ABC efflux transporter of multiple drugs CDR1

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Supramolecule #1: Apo Cdr1

SupramoleculeName: Apo Cdr1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candida albicans SC5314 (yeast)

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Macromolecule #1: Pleiotropic ABC efflux transporter of multiple drugs CDR1

MacromoleculeName: Pleiotropic ABC efflux transporter of multiple drugs CDR1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans SC5314 (yeast)
Molecular weightTheoretical: 170.159656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSDSKMSSQD ESKLEKAISQ DSSSENHSIN EYHGFDAHTS ENIQNLARTF THDSFKDDSS AGLLKYLTHM SEVPGVNPYE HEEINNDQL NPDSENFNAK FWVKNLRKLF ESDPEYYKPS KLGIGYRNLR AYGVANDSDY QPTVTNALWK LATEGFRHFQ K DDDSRYFD ...String:
MSDSKMSSQD ESKLEKAISQ DSSSENHSIN EYHGFDAHTS ENIQNLARTF THDSFKDDSS AGLLKYLTHM SEVPGVNPYE HEEINNDQL NPDSENFNAK FWVKNLRKLF ESDPEYYKPS KLGIGYRNLR AYGVANDSDY QPTVTNALWK LATEGFRHFQ K DDDSRYFD ILKSMDAIMR PGELTVVLGR PGAGCSTLLK TIAVNTYGFH IGKESQITYD GLSPHDIERH YRGDVIYSAE TD VHFPHLS VGDTLEFAAR LRTPQNRGEG IDRETYAKHM ASVYMATYGL SHTRNTNVGN DFVRGVSGGE RKRVSIAEAS LSG ANIQCW DNATRGLDSA TALEFIRALK TSAVILDTTP LIAIYQCSQD AYDLFDKVVV LYEGYQIFFG KATKAKEYFE KMGW KCPQR QTTADFLTSL TNPAEREPLP GYEDKVPRTA QEFETYWKNS PEYAELTKEI DEYFVECERS NTRETYRESH VAKQS NNTR PASPYTVSFF MQVRYGVARN FLRMKGDPSI PIFSVFGQLV MGLILSSVFY NLSQTTGSFY YRGAAMFFAV LFNAFS SLL EIMSLFEARP IVEKHKKYAL YRPSADALAS IISELPVKLA MSMSFNFVFY FMVNFRRNPG RFFFYWLMCI WCTFVMS HL FRSIGAVSTS ISGAMTPATV LLLAMVIYTG FVIPTPSMLG WSRWINYINP VGYVFESLMV NEFHGREFQC AQYVPSGP G YENISRSNQV CTAVGSVPGN EMVSGTNYLA GAYQYYNSHK WRNLGITIGF AVFFLAIYIA LTEFNKGAMQ KGEIVLFLK GSLKKHKRKT AASNKGDIEA GPVAGKLDYQ DEAEAVNNEK FTEKGSTGSV DFPENREIFF WRDLTYQVKI KKEDRVILDH VDGWVKPGQ ITALMGASGA GKTTLLNCLS ERVTTGIITD GERLVNGHAL DSSFQRSIGY VQQQDVHLET TTVREALQFS A YLRQSNKI SKKEKDDYVD YVIDLLEMTD YADALVGVAG EGLNVEQRKR LTIGVELVAK PKLLLFLDEP TSGLDSQTAW SI CKLMRKL ADHGQAILCT IHQPSALIMA EFDRLLFLQK GGRTAYFGEL GENCQTMINY FEKYGADPCP KEANPAEWML QVV GAAPGS HAKQDYFEVW RNSSEYQAVR EEINRMEAEL SKLPRDNDPE ALLKYAAPLW KQYLLVSWRT IVQDWRSPGY IYSK IFLVV SAALFNGFSF FKAKNNMQGL QNQMFSVFMF FIPFNTLVQQ MLPYFVKQRD VYEVREAPSR TFSWFAFIAG QITSE IPYQ VAVGTIAFFC WYYPLGLYNN ATPTDSVNPR GVLMWMLVTA FYVYTATMGQ LCMSFSELAD NAANLATLLF TMCLNF CGV LAGPDVLPGF WIFMYRCNPF TYLVQAMLST GLANTFVKCA EREYVSVKPP NGESCSTYLD PYIKFAGGYF ETRNDGS CA FCQMSSTNTF LKSVNSLYSE RWRNFGIFIA FIAINIILTV IFYWLARVPK GNREKKNKK

UniProtKB: Pleiotropic ABC efflux transporter of multiple drugs CDR1

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 410230
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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