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- PDB-3g61: Structure of P-glycoprotein Reveals a Molecular Basis for Poly-Sp... -

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Basic information

Entry
Database: PDB / ID: 3g61
TitleStructure of P-glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding
ComponentsMultidrug resistance protein 1aMultiple drug resistance
KeywordsMEMBRANE PROTEIN / P-glycoprotein / Pgp / multidrug resistance / cycle peptides / ATP-binding / Nucleotide-binding
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 / response to quercetin / cellular response to external biotic stimulus ...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 / response to quercetin / cellular response to external biotic stimulus / regulation of intestinal absorption / response to antineoplastic agent / Prednisone ADME / positive regulation of establishment of Sertoli cell barrier / ceramide translocation / terpenoid transport / ceramide floppase activity / response to glycoside / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / regulation of response to osmotic stress / cellular response to L-glutamate / ABC-family proteins mediated transport / establishment of blood-brain barrier / response to thyroxine / phosphatidylcholine floppase activity / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / xenobiotic detoxification by transmembrane export across the plasma membrane / export across plasma membrane / response to vitamin D / ABC-type xenobiotic transporter / intercellular canaliculus / transepithelial transport / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / response to vitamin A / response to glucagon / intestinal absorption / phospholipid translocation / cellular response to antibiotic / maintenance of blood-brain barrier / cellular hyperosmotic salinity response / cellular response to alkaloid / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / placenta development / regulation of chloride transport / stem cell proliferation / cellular response to estradiol stimulus / brush border membrane / circadian rhythm / G2/M transition of mitotic cell cycle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ubiquitin protein ligase binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
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. ...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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-2J8 / ATP-dependent translocase ABCB1 / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.35 Å
AuthorsAller, S.G. / Yu, J. / Ward, A. / Weng, Y. / Chittaboina, S. / Zhuo, R. / Harrell, P.M. / Trinh, Y.T. / Zhang, Q. / Urbatsch, I.L. / Chang, G.
CitationJournal: Science / Year: 2009
Title: Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding.
Authors: Aller, S.G. / Yu, J. / Ward, A. / Weng, Y. / Chittaboina, S. / Zhuo, R. / Harrell, P.M. / Trinh, Y.T. / Zhang, Q. / Urbatsch, I.L. / Chang, G.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2013Group: Atomic model
Revision 1.3Oct 21, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation ...chem_comp / diffrn_radiation / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _diffrn_radiation.monochromator ..._chem_comp.pdbx_synonyms / _diffrn_radiation.monochromator / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance protein 1a
B: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,5456
Polymers283,7962
Non-polymers2,7504
Water0
1
A: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2733
Polymers141,8981
Non-polymers1,3752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2733
Polymers141,8981
Non-polymers1,3752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.742, 114.978, 375.810
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 / Multiple drug resistance / MCG1178


Mass: 141897.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, mCG_1178 / References: UniProt: Q5I1Y5, UniProt: P21447*PLUS
#2: Chemical
ChemComp-2J8 / (4S,11S,18S)-4,11,18-tri(propan-2-yl)-6,13,20-triselena-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1~5,8~.1~12,15~]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione / cyclic-tris-(S)-valineselenazole / QZ59-SSS


Mass: 687.413 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30N6O3Se3

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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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 20-23% PEG400, 0.05M TRIS, 0.04% sodium cholate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97854 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 4.35→20 Å / Num. all: 28391 / Num. obs: 26489 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 103.5 Å2
Reflection shellResolution: 4.35→4.62 Å / % possible all: 85.3

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.35→19.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 120841.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.356 2642 10 %RANDOM
Rwork0.308 ---
obs0.308 26489 93.3 %-
all-28391 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.2196 Å2 / ksol: 0.15 e/Å3
Displacement parametersBiso mean: 182.6 Å2
Baniso -1Baniso -2Baniso -3
1--16.49 Å20 Å20 Å2
2--50.71 Å20 Å2
3----34.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.15 Å0.91 Å
Luzzati d res low-20 Å
Luzzati sigma a1.33 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 4.35→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18342 0 106 0 18448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it13.951.5
X-RAY DIFFRACTIONc_mcangle_it21.612
X-RAY DIFFRACTIONc_scbond_it15.022
X-RAY DIFFRACTIONc_scangle_it21.742.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 4.35→4.62 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.498 376 9.4 %
Rwork0.46 3624 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2QZ59SSS.par

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