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- EMDB-39908: Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-39908
TitleCryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (apo-form)
Map data
Sample
  • Complex: Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (apo-form)
    • Protein or peptide: ATP-binding cassette sub-family C member 4
  • Ligand: CHOLESTEROL
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsATP-binding cassette sub-family C member 4 / Multidrug resistance proteins (MRPs) / multidrug-resistance (MDR) / TRANSPORT PROTEIN / membrane protein
Function / homology
Function and homology information


15-hydroxyprostaglandin dehydrogenase (NAD+) activity / purine nucleotide transmembrane transporter activity / cAMP transport / guanine nucleotide transmembrane transporter activity / ABC-type bile acid transporter activity / platelet dense granule membrane / platelet degranulation / leukotriene transport / prostaglandin transport / ABC-type glutathione S-conjugate transporter activity ...15-hydroxyprostaglandin dehydrogenase (NAD+) activity / purine nucleotide transmembrane transporter activity / cAMP transport / guanine nucleotide transmembrane transporter activity / ABC-type bile acid transporter activity / platelet dense granule membrane / platelet degranulation / leukotriene transport / prostaglandin transport / ABC-type glutathione S-conjugate transporter activity / urate transport / ABC-type glutathione-S-conjugate transporter / glutathione transmembrane transporter activity / prostaglandin transmembrane transporter activity / urate transmembrane transporter activity / ATPase-coupled inorganic anion transmembrane transporter activity / external side of apical plasma membrane / xenobiotic transmembrane transport / prostaglandin secretion / export across plasma membrane / Paracetamol ADME / ABC-type xenobiotic transporter / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / Azathioprine ADME / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / cilium assembly / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transport across blood-brain barrier / xenobiotic metabolic process / ABC-family proteins mediated transport / transmembrane transport / Platelet degranulation / basolateral plasma membrane / apical plasma membrane / intracellular membrane-bounded organelle / nucleolus / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ATP-binding cassette sub-family C member 4 / : / : / 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 ...ATP-binding cassette sub-family C member 4 / : / : / 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
ATP-binding cassette sub-family C member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsXie Z / Long F
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0909500 China
CitationJournal: To Be Published
Title: Structural insights into the human MRP4 mediating multiple drug resistance (MDR) to vincristine and 5-FU and reversal of MDR by lapatinib
Authors: Xie Z / Long F
History
DepositionApr 27, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39908.png

Downloads & links

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Map

FileDownload / File: emd_39908.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.3666391 - 1.793251
Average (Standard dev.)0.0020808 (±0.043280106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39908_msk_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_39908_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39908_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (...

EntireName: Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (apo-form)
Components
  • Complex: Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (apo-form)
    • Protein or peptide: ATP-binding cassette sub-family C member 4
  • Ligand: CHOLESTEROL
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (...

SupramoleculeName: Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (apo-form)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP-binding cassette sub-family C member 4

MacromoleculeName: ATP-binding cassette sub-family C member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 152.203547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HMLPVYQEVK PNPLQDANLC SRVFFWWLNP LFKIGHKRRL EEDDMYSVLP EDRSQHLGEE LQGFWDKEVL RAENDAQKP SLTRAIIKCY WKSYLVLGIF TLIEESAKVI QPIFLGKIIN YFENYDPMDS VALNTAYAYA TVLTFCTLIL A ILHHLYFY ...String:
MHHHHHHHHH HMLPVYQEVK PNPLQDANLC SRVFFWWLNP LFKIGHKRRL EEDDMYSVLP EDRSQHLGEE LQGFWDKEVL RAENDAQKP SLTRAIIKCY WKSYLVLGIF TLIEESAKVI QPIFLGKIIN YFENYDPMDS VALNTAYAYA TVLTFCTLIL A ILHHLYFY HVQCAGMRLR VAMCHMIYRK ALRLSNMAMG KTTTGQIVNL LSNDVNKFDQ VTVFLHFLWA GPLQAIAVTA LL WMEIGIS CLAGMAVLII LLPLQSCFGK LFSSLRSKTA TFTDARIRTM NEVITGIRII KMYAWEKSFS NLITNLRKKE ISK ILRSSC LRGMNLASFF SASKIIVFVT FTTYVLLGSV ITASRVFVAV TLYGAVRLTV TLFFPSAIER VSEAIVSIRR IQTF LLLDE ISQRNRQLPS DGKKMVHVQD FTAFWDKASE TPTLQGLSFT VRPGELLAVV GPVGAGKSSL LSAVLGELAP SHGLV SVHG RIAYVSQQPW VFSGTLRSNI LFGKKYEKER YEKVIKACAL KKDLQLLEDG DLTVIGDRGT TLSGGQKARV NLARAV YQD ADIYLLDDPL SAVDAEVSRH LFELCICQIL HEKITILVTH QLQYLKAASQ ILILKDGKMV QKGTYTEFLK SGIDFGS LL KKDNEESEQP PVPGTPTLRN RTFSESSVWS QQSSRPSLKD GALESQDTEN VPVTLSEENR SEGKVGFQAY KNYFRAGA H WIVFIFLILL NTAAQVAYVL QDWWLSYWAN KQSMLNVTVN GGGNVTEKLD LNWYLGIYSG LTVATVLFGI ARSLLVFYV LVNSSQTLHN KMFESILKAP VLFFDRNPIG RILNRFSKDI GHLDDLLPLT FLDFIQTLLQ VVGVVSVAVA VIPWIAIPLV PLGIIFIFL RRYFLETSRD VKRLESTTRS PVFSHLSSSL QGLWTIRAYK AEERCQELFD AHQDLHSEAW FLFLTTSRWF A VRLDAICA MFVIIVAFGS LILAKTLDAG QVGLALSYAL TLMGMFQWCV RQSAEVENMM ISVERVIEYT DLEKEAPWEY QK RPPPAWP HEGVIIFDNV NFMYSPGGPL VLKHLTALIK SQEKVGIVGR TGAGKSSLIS ALFRLSEPEG KIWIDKILTT EIG LHDLRK KMSIIPQEPV LFTGTMRKNL DPFNEHTDEE LWNALQEVQL KETIEDLPGK MDTELAESGS NFSVGQRQLV CLAR AILRK NQILIIDEAT ANVDPRTDEL IQKKIREKFA HCTVLTIAHR LNTIIDSDKI MVLDSGRLKE YDEPYVLLQN KESLF YKMV QQLGKAEAAA LTETAKQVYF KRNYPHIGHT DHMVTNTSNG QPSTLTIFET ALDYKDDDDK

UniProtKB: ATP-binding cassette sub-family C member 4

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU (ver. Version 3.2.0.4776REL)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 540659
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8zbr:
Cryo-EM structure of nanodisc-reconstituted wildtype human MRP4 (apo-form)

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