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- PDB-4ksc: Structures of P-glycoprotein reveal its conformational flexibilit... -

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Basic information

Entry
Database: PDB / ID: 4ksc
TitleStructures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain
ComponentsMultidrug resistance protein 1A
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / transporter / ATP binding / membrane
Function / homology
Function and homology information


hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / negative regulation of sensory perception of pain / regulation of intestinal absorption ...hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / negative regulation of sensory perception of pain / regulation of intestinal absorption / response to quercetin / cellular response to external biotic stimulus / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / ceramide translocation / establishment of blood-retinal barrier / protein localization to bicellular tight junction / response to alcohol / ABC-family proteins mediated transport / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / cellular response to L-glutamate / intercellular canaliculus / export across plasma membrane / ABC-type xenobiotic transporter / response to vitamin D / P-type phospholipid transporter / response to vitamin A / ABC-type xenobiotic transporter activity / intestinal absorption / response to glucagon / phospholipid translocation / cellular response to antibiotic / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / cellular response to estradiol stimulus / response to progesterone / female pregnancy / brush border membrane / placenta development / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / 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 transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsWard, A. / Szewczyk, P. / Grimard, V. / Lee, C.-W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. ...Ward, A. / Szewczyk, P. / Grimard, V. / Lee, C.-W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. / Swartz, D.J. / Falson, P. / Urbatsch, I. / Govaerts, C. / Steyaert, J. / Chang, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain.
Authors: Ward, A.B. / Szewczyk, P. / Grimard, V. / Lee, C.W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. / Swartz, D.J. / Falson, P.G. / Urbatsch, I.L. / Govaerts, ...Authors: Ward, A.B. / Szewczyk, P. / Grimard, V. / Lee, C.W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. / Swartz, D.J. / Falson, P.G. / Urbatsch, I.L. / Govaerts, C. / Steyaert, J. / Chang, G.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Sep 9, 2015Group: Structure summary
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance protein 1A


Theoretical massNumber of molelcules
Total (without water)141,8781
Polymers141,8781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.650, 138.290, 194.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multidrug resistance protein 1A / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 3 / P-glycoprotein 3


Mass: 141877.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25-29.5% w/v PEG 600, 50 mM LiSO4, 10 mM EDTA, 100 mM Hepes, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4→112.749 Å / Num. all: 22399 / Num. obs: 19465 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
CNSrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→112.749 Å / SU ML: 0.78 / σ(F): 2.02 / Phase error: 35.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3377 904 4.87 %RANDOM
Rwork0.3158 ---
obs0.317 18561 86.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→112.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9171 0 0 0 9171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049340
X-RAY DIFFRACTIONf_angle_d0.90912628
X-RAY DIFFRACTIONf_dihedral_angle_d12.7823395
X-RAY DIFFRACTIONf_chiral_restr0.0361456
X-RAY DIFFRACTIONf_plane_restr0.0041606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.25060.37941550.33833008X-RAY DIFFRACTION90
4.2506-4.57880.37751360.32732729X-RAY DIFFRACTION82
4.5788-5.03960.37321670.31683104X-RAY DIFFRACTION93
5.0396-5.76880.33391450.32362982X-RAY DIFFRACTION89
5.7688-7.2680.36091440.32582956X-RAY DIFFRACTION87
7.268-112.79350.28421570.29242878X-RAY DIFFRACTION81

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