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- PDB-9jc0: Multidrug resistance-associated protein 2 in complex with MK-571 ... -

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Basic information

Entry
Database: PDB / ID: 9jc0
TitleMultidrug resistance-associated protein 2 in complex with MK-571 and ATP
ComponentsATP-binding cassette sub-family C member 2
KeywordsTRANSPORT PROTEIN / ATP-binding cassette transporter / 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
: / ADENOSINE-5'-TRIPHOSPHATE / ATP-binding cassette sub-family C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsYun, C.H. / Zhao, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Multidrug resistance-associated protein 2 in complex with MK-571 and ATP
Authors: Yun, C.H. / Zhao, P.
History
DepositionAug 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-binding cassette sub-family C member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,9706
Polymers174,3921
Non-polymers1,5785
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 ATP-binding cassette sub-family C member 2 / Canalicular multidrug resistance protein / Canalicular multispecific organic anion transporter 1 / ...Canalicular multidrug resistance protein / Canalicular multispecific organic anion transporter 1 / Multidrug resistance-associated protein 2


Mass: 174392.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCC2, CMOAT, CMOAT1, CMRP, MRP2 / Production host: Homo sapiens (human)
References: UniProt: Q92887, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate, ABC-type xenobiotic transporter, ABC-type ...References: UniProt: Q92887, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate, ABC-type xenobiotic transporter, ABC-type glutathione-S-conjugate transporter
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1E61 / Verlukast / 3-[(~{R})-[3-[(~{E})-2-(7-chloranylquinolin-2-yl)ethenyl]phenyl]-[3-(dimethylamino)-3-oxidanylidene-propyl]sulfanyl-methyl]sulfanylpropanoic acid


Mass: 515.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27ClN2O3S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Multidrug resistance-associated protein 2 with MK-571 and ATP
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87222 / Symmetry type: POINT

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