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- PDB-3g60: Structure of P-glycoprotein Reveals a Molecular Basis for Poly-Sp... -

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Basic information

Entry
Database: PDB / ID: 3g60
TitleStructure of P-glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding
ComponentsMultidrug resistance protein 1a
KeywordsMEMBRANE PROTEIN / P-glycoprotein / Pgp / multidrug resistance / cyclic peptide
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 / ABC-type xenobiotic transporter activity / response to vitamin A / 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
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-0JZ / ATP-dependent translocase ABCB1 / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 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 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)285,1714
Polymers283,7962
Non-polymers1,3752
Water00
1
A: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5852
Polymers141,8981
Non-polymers6871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5852
Polymers141,8981
Non-polymers6871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.629, 115.090, 374.204
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 / 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-0JZ / (4R,11R,18R)-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-(R)-valineselenazole / QZ59-RRR


Mass: 687.413 Da / Num. of mol.: 2 / 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: 3.67 Å3/Da / Density % sol: 66.45 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 4.4→20 Å / Num. all: 27007 / Num. obs: 25576 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 121.9 Å2 / Rsym value: 0.073
Reflection shellResolution: 4.4→4.67 Å / % possible all: 90.1

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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: 4.4→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 215488.07 / 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
Rfree0.365 2562 10 %RANDOM
Rwork0.314 ---
all0.314 27007 --
obs0.314 25576 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 119.909 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 198.8 Å2
Baniso -1Baniso -2Baniso -3
1--14.79 Å20 Å20 Å2
2--50.27 Å20 Å2
3----35.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.23 Å0.92 Å
Luzzati d res low-20 Å
Luzzati sigma a1.2 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 4.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18342 0 72 0 18414
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it20.521.5
X-RAY DIFFRACTIONc_mcangle_it31.792
X-RAY DIFFRACTIONc_scbond_it20.792
X-RAY DIFFRACTIONc_scangle_it30.532.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 4.4→4.67 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.472 402 10.2 %
Rwork0.421 3554 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2QZ59RRR.paramQZ59RRR.top

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