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- PDB-3g5u: Structure of P-glycoprotein Reveals a Molecular Basis for Poly-Sp... -

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Basic information

Entry
Database: PDB / ID: 3g5u
TitleStructure of P-glycoprotein Reveals a Molecular Basis for Poly-Specific Drug Binding
ComponentsMultidrug resistance protein 1a
KeywordsMEMBRANE PROTEIN / P-glycoprotein / multidrug resistance / Pgp / 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 / 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 / negative regulation of sensory perception of pain / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / response to alcohol / ceramide translocation / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / ABC-type oligopeptide transporter activity / ABC-family proteins mediated transport / cellular response to L-glutamate / 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 / intercellular canaliculus / export across plasma membrane / response to vitamin D / ABC-type xenobiotic transporter / P-type phospholipid transporter / response to vitamin A / ABC-type xenobiotic transporter activity / response to glucagon / intestinal absorption / 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 / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.8 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 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)286,13914
Polymers283,7322
Non-polymers2,40712
Water00
1
A: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0697
Polymers141,8661
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multidrug resistance protein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0697
Polymers141,8661
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.542, 115.426, 378.858
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: 141865.844 Da / Num. of mol.: 2 / Mutation: C952A
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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg

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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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17% PEG 350mme, 0.05M tris, 0.04% sodium cholate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.00695, 1.00923
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 16, 2007
RadiationMonochromator: APS mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.006951
21.009231
ReflectionResolution: 3.8→50 Å / Num. all: 42800 / Num. obs: 41131 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 48 Å2 / Rsym value: 0.082

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.8→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 148683.32 / 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
Rfree0.347 4203 10.2 %RANDOM
Rwork0.306 ---
obs0.306 41131 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.0058 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 136.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--26.39 Å20 Å2
3----26.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.93 Å0.76 Å
Luzzati d res low-20 Å
Luzzati sigma a0.98 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 3.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18340 0 12 0 18352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.15
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.486 636 10.4 %
Rwork0.448 5472 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param

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