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- EMDB-61373: Multidrug resistance-associated protein 2 in complex with MK-571 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61373
TitleMultidrug resistance-associated protein 2 in complex with MK-571
Map data
Sample
  • Complex: monomer of Multidrug resistance-associated protein 2 with MK-571
    • Protein or peptide: ATP-binding cassette sub-family C member 2
  • Ligand: 3-[(~{S})-[3-[(~{E})-2-(7-chloranylquinolin-2-yl)ethenyl]phenyl]-[3-(dimethylamino)-3-oxidanylidene-propyl]sulfanyl-methyl]sulfanylpropanoic acid
KeywordsATP-binding cassette transporter / TRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective ABCC2 causes DJS / mercury ion transport / glucuronoside transport / response to cisplatin / proximal tubule development / xenobiotic export from cell / response to wortmannin / bilirubin transmembrane transporter activity / glutathione transport / mRNA metabolic process ...Defective ABCC2 causes DJS / mercury ion transport / glucuronoside transport / response to cisplatin / proximal tubule development / xenobiotic export from cell / response to wortmannin / bilirubin transmembrane transporter activity / glutathione transport / mRNA metabolic process / leukotriene transport / toxin transmembrane transporter activity / response to peptide / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / : / heme catabolic process / Atorvastatin ADME / bilirubin transport / xenobiotic transport across blood-brain barrier / intercellular canaliculus / : / xenobiotic transmembrane transport / Paracetamol ADME / cardiac muscle cell differentiation / xenobiotic detoxification by transmembrane export across the plasma membrane / transepithelial transport / ABC-type xenobiotic transporter / response to growth hormone / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / Heme degradation / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / Aspirin ADME / ATPase-coupled transmembrane transporter activity / xenobiotic transmembrane transporter activity / ABC-type transporter activity / transport across blood-brain barrier / xenobiotic metabolic process / glutathione metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to insulin / ABC-family proteins mediated transport / transmembrane transport / vesicle / gene expression / apical plasma membrane / negative regulation of gene expression / cell surface / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / 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. ...Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsYun CH / Zhao P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471256 China
CitationJournal: To Be Published
Title: Multidrug resistance-associated protein 2 in complex with MK-571
Authors: Yun CH / Zhao P
History
DepositionAug 30, 2024-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61373.png

Downloads & links

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Map

FileDownload / File: emd_61373.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.5541288 - 0.9639128
Average (Standard dev.)-0.00011230886 (±0.019906227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61373_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61373_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 : monomer of Multidrug resistance-associated protein 2 with MK-571

EntireName: monomer of Multidrug resistance-associated protein 2 with MK-571
Components
  • Complex: monomer of Multidrug resistance-associated protein 2 with MK-571
    • Protein or peptide: ATP-binding cassette sub-family C member 2
  • Ligand: 3-[(~{S})-[3-[(~{E})-2-(7-chloranylquinolin-2-yl)ethenyl]phenyl]-[3-(dimethylamino)-3-oxidanylidene-propyl]sulfanyl-methyl]sulfanylpropanoic acid

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Supramolecule #1: monomer of Multidrug resistance-associated protein 2 with MK-571

SupramoleculeName: monomer of Multidrug resistance-associated protein 2 with MK-571
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 2

MacromoleculeName: ATP-binding cassette sub-family C member 2 / 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: 174.392344 KDa
SequenceString: MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGYL WLLAPWQLLH VYKSRTKRSS TTKLYLAKQV FVGFLLILAA IELALVLTE DSGQATVPAV RYTNPSLYLG TWLLVLLIQY SRQWCVQKNS WFLSLFWILS ILCGTFQFQT LIRTLLQGDN S NLAYSCLF ...String:
MLEKFCNSTF WNSSFLDSPE ADLPLCFEQT VLVWIPLGYL WLLAPWQLLH VYKSRTKRSS TTKLYLAKQV FVGFLLILAA IELALVLTE DSGQATVPAV RYTNPSLYLG TWLLVLLIQY SRQWCVQKNS WFLSLFWILS ILCGTFQFQT LIRTLLQGDN S NLAYSCLF FISYGFQILI LIFSAFSENN ESSNNPSSIA SFLSSITYSW YDSIILKGYK RPLTLEDVWE VDEEMKTKTL VS KFETHMK RELQKARRAL QRRQEKSSQQ NSGARLPGLN KNQSQSQDAL VLEDVEKKKK KSGTKKDVPK SWLMKALFKT FYM VLLKSF LLKLVNDIFT FVSPQLLKLL ISFASDRDTY LWIGYLCAIL LFTAALIQSF CLQCYFQLCF KLGVKVRTAI MASV YKKAL TLSNLARKEY TVGETVNLMS VDAQKLMDVT NFMHMLWSSV LQIVLSIFFL WRELGPSVLA GVGVMVLVIP INAIL STKS KTIQVKNMKN KDKRLKIMNE ILSGIKILKY FAWEPSFRDQ VQNLRKKELK NLLAFSQLQC VVIFVFQLTP VLVSVV TFS VYVLVDSNNI LDAQKAFTSI TLFNILRFPL SMLPMMISSM LQASVSTERL EKYLGGDDLD TSAIRHDCNF DKAMQFS EA SFTWEHDSEA TVRDVNLDIM AGQLVAVIGP VGSGKSSLIS AMLGEMENVH GHITIKGTTA YVPQQSWIQN GTIKDNIL F GTEFNEKRYQ QVLEACALLP DLEMLPGGDL AEIGEKGINL SGGQKQRISL ARATYQNLDI YLLDDPLSAV DAHVGKHIF NKVLGPNGLL KGKTRLLVTH SMHFLPQVDE IVVLGNGTIV EKGSYSALLA KKGEFAKNLK TFLRHTGPEE EATVHDGSEE EDDDYGLIS SVEEIPEDAA SITMRRENSF RRTLSRSSRS NGRHLKSLRN SLKTRNVNSL KEDEELVKGQ KLIKKEFIET G KVKFSIYL EYLQAIGLFS IFFIILAFVM NSVAFIGSNL WLSAWTSDSK IFNSTDYPAS QRDMRVGVYG ALGLAQGIFV FI AHFWSAF GFVHASNILH KQLLNNILRA PMRFFDTTPT GRIVNRFAGD ISTVDDTLPQ SLRSWITCFL GIISTLVMIC MAT PVFTII VIPLGIIYVS VQMFYVSTSR QLRRLDSVTR SPIYSHFSET VSGLPVIRAF EHQQRFLKHN EVRIDTNQKC VFSW ITSNR WLAIRLELVG NLTVFFSALM MVIYRDTLSG DTVGFVLSNA LNITQTLNWL VRMTSEIETN IVAVERITEY TKVEN EAPW VTDKRPPPDW PSKGKIQFNN YQVRYRPELD LVLRGITCDI GSMEKIGVVG RTGAGKSSLT NCLFRILEAA GGQIII DGV DIASIGLHDL REKLTIIPQD PILFSGSLRM NLDPFNNYSD EEIWKALELA HLKSFVASLQ LGLSHEVTEA GGNLSIG QR QLLCLGRALL RKSKILVLDE ATAAVDLETD NLIQTTIQNE FAHCTVITIA HRLHTIMDSD KVMVLDNGKI IECGSPEE L LQIPGPFYFM AKEAGIENVN STKF

UniProtKB: ATP-binding cassette sub-family C member 2

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Macromolecule #2: 3-[(~{S})-[3-[(~{E})-2-(7-chloranylquinolin-2-yl)ethenyl]phenyl]-...

MacromoleculeName: 3-[(~{S})-[3-[(~{E})-2-(7-chloranylquinolin-2-yl)ethenyl]phenyl]-[3-(dimethylamino)-3-oxidanylidene-propyl]sulfanyl-methyl]sulfanylpropanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EIX
Molecular weightTheoretical: 515.087 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 76597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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