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- EMDB-54488: CgCdr1 in complex with ATP, ADP-VO4 -

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Basic information

Entry
Database: EMDB / ID: EMD-54488
TitleCgCdr1 in complex with ATP, ADP-VO4
Map data
Sample
  • Complex: Cdr1 purified in detergent complexed with ATP and ADP-Mg-VO4
    • Protein or peptide: Pleiotropic ABC efflux transporter of multiple drugs CDR1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ERGOSTEROL
  • Ligand: water
KeywordsCdr1 / multidrug transporter / drug resistance / ABC transporter / Candida glabrata / TRANSPORT PROTEIN
Function / homology
Function and homology information


azole transmembrane transport / vacuolar lumen / intracellular monoatomic cation homeostasis / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter activity / cellular response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / identical protein binding / 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 speciesNakaseomyces glabratus (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPata J / Zarkadas E / Schoehn G / Chaptal V / Falson P
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-24-CE44-xxxx-xx France
CitationJournal: To Be Published
Title: CgCdr1 in complex with ATP, ADP-VO4
Authors: Pata J / Zarkadas E / Schoehn G / Chaptal V / Falson P
History
DepositionJul 21, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54488.png

Downloads & links

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Map

FileDownload / File: emd_54488.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.176 Å		0.84 Å/pix.
x 384 pix.
= 322.176 Å		0.84 Å/pix.
x 384 pix.
= 322.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.084827 - 4.2582464
Average (Standard dev.)0.0010813912 (±0.06260721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54488_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54488_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cdr1 purified in detergent complexed with ATP and ADP-Mg-VO4

EntireName: Cdr1 purified in detergent complexed with ATP and ADP-Mg-VO4
Components
  • Complex: Cdr1 purified in detergent complexed with ATP and ADP-Mg-VO4
    • Protein or peptide: Pleiotropic ABC efflux transporter of multiple drugs CDR1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: VANADATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ERGOSTEROL
  • Ligand: water

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Supramolecule #1: Cdr1 purified in detergent complexed with ATP and ADP-Mg-VO4

SupramoleculeName: Cdr1 purified in detergent complexed with ATP and ADP-Mg-VO4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nakaseomyces glabratus (fungus)
Molecular weightTheoretical: 170 KDa

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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: Nakaseomyces glabratus (fungus)
Molecular weightTheoretical: 170.5945 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSLASDKKDA DVASTTTTAQ DDDNLSTYHG FDHHVQDQVR QLARTLTQQS SLHQKKEHTL PEEGINPIFT NTEADDYNPR LDPTSDEFS SAEWVQNMSN ISNSDPDYYK PYSLGCYWKD LVATGESADI EYQANFLNGP YKGLKTVYNT VVPSTASSKD K NFKILKSM ...String:
MSLASDKKDA DVASTTTTAQ DDDNLSTYHG FDHHVQDQVR QLARTLTQQS SLHQKKEHTL PEEGINPIFT NTEADDYNPR LDPTSDEFS SAEWVQNMSN ISNSDPDYYK PYSLGCYWKD LVATGESADI EYQANFLNGP YKGLKTVYNT VVPSTASSKD K NFKILKSM EGAVNPGELL VVLGRPGSGC TTLLKSISSN THGFNIAKES TISYSGMTPN DIRKHFRGEV VYNAEADIHL PH LTVYQTL LTVARLKTPQ NRLKGIDRET YARHLTEVAM ATFGLSHTRN TKVGNDLVRG VSGGERKRVS IAEVSICGSK FQC WDNATR GLDSATALEF IRALKVQASI SNAAATVAIY QCSQDAYDLF DKVCVLYDGY QIYFGPAGKA KEYFQKMGYV SPER QTTAD FLTAVTSPSE RIINQDYINR GIFVPQTPKE MWEYWRASED HADLIKEIDS KLSDNYDANL AEIKDAHVAR QSKRA RPSS PYTVSYGMQI KYLLIRNFWR IKQSSGVTLF MVIGNSSMAF ILGSMFYKVM KHNTTSTFYF RGAAMFFAVL FNAFSS LLE IFSLFEARPI TEKHRTYSLY HPSADAFASI LSEVPAKLIT AVCFNIIYYF LVNFRRNGGV FFFYFLINIV AVFAMSH LF RCVGSVSKTL SAAMVPASML LLGLSMYSGF AIPRTKILGW SKWIWYINPL AYLFESLMIN EFHDRKFPCS QYIPSGSV Y NNVPADSRIC SSVGAIRGND YVLGDDFLRE SYSYLHKHKW RGFGIGLAYV IFFLVLYLIL CEYNEGAKQK GEILVFPQN IVRRMKKERK LKNVSSDNDV EIGDVSDISD KKILADSSDE SEESGANIGL SQSEAIFHWR NLCYDVQIKK ETRRILNNVD GWVKPGTLT ALMGASGAGK TTLLDCLAER VTMGVITGEV SVDGKQRDDS FARSIGYCQQ QDLHLKTSTV RESLRFSAYL R QPADVSIE EKNQYVEDVI KILEMEQYAD AVVGVPGEGL NVEQRKRLTI GVELAAKPKL LVFLDEPTSG LDSQTAWSIC QL MKKLANH GQAILCTIHQ PSAILMQEFD RLLFLQRGGK TVYFGDLGDG CKTMIDYFES HGSHKCPPDA NPAEWMLEVV GAA PGSHAN QDYHEVWRNS DEYQKVQEEL EWMSNELPKK NTNNSETVHK EFATGVLYQC KLVSLRLFQQ YWRSPDYLWS KFFL TIFNN IFIGFTFFKA DRSLQGLQNQ MLAVFMFTVI FNPLLQQYLP SFVQQRDLYE ARERPSRTFS WKAFIVSQIL VEIPW NILA GTVAFVIYYY AIGFYSNASV AHQLHERGAL FWLFSCAFYV YIGSLALFCI SFNQVAEAAA NMASLMFTLS LSFCGV LVT PNGMPRFWIF MYRVSPLTYL IDGMLSTGVA NVAIKCSNYE LLRFSPAANL TCGEYLGPYL QTVKTGYIVD PSATDTC EL CPYSHTNDFL SSVSSKYSRR WRNWGIFICY IAFNYIAGIF LYWLARVPKK SGKLAKKGGR HHHHHH

UniProtKB: Pleiotropic ABC efflux transporter of multiple drugs CDR1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 6 / Number of copies: 8 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 22 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration7 mg/mL
BufferpH: 7.5
Details: 50 mM HEPES-HCl, pH 7.5, 100 mM NaCl, 70 uM PCC, 4 uM DCOD
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 191450
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9s2c:
CgCdr1 in complex with ATP, ADP-VO4

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