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- PDB-6ujr: P-glycoprotein mutant-F724A and C952A-with BDE100 -

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Basic information

Entry
Database: PDB / ID: 6ujr
TitleP-glycoprotein mutant-F724A and C952A-with BDE100
ComponentsATP-dependent translocase ABCB1
KeywordsTRANSLOCASE / P-glycoprotein / MDR1 / P-gp / Pgp / Multidrug Resistance Protein
Function / homology
Function and homology information


Atorvastatin ADME / Prednisone ADME / hormone transport / cellular response to nonylphenol / cellular response to borneol / response to codeine / response to cyclosporin A / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug ...Atorvastatin ADME / Prednisone ADME / hormone transport / cellular response to nonylphenol / cellular response to borneol / response to codeine / response to cyclosporin A / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / terpenoid transport / ceramide floppase activity / negative regulation of sensory perception of pain / positive regulation of establishment of Sertoli cell barrier / regulation of intestinal absorption / cellular response to external biotic stimulus / response to quercetin / response to antineoplastic agent / ceramide translocation / floppase activity / ABC-family proteins mediated transport / establishment of blood-retinal barrier / phosphatidylethanolamine flippase activity / protein localization to bicellular tight junction / phosphatidylcholine floppase activity / xenobiotic transport across blood-brain barrier / response to thyroxine / establishment of blood-brain barrier / intercellular canaliculus / xenobiotic detoxification by transmembrane export across the plasma membrane / export across plasma membrane / P-type phospholipid transporter / cellular response to L-glutamate / response to vitamin A / ABC-type xenobiotic transporter / response to vitamin D / response to glycoside / response to alcohol / response to glucagon / intestinal absorption / ABC-type xenobiotic transporter activity / cellular response to antibiotic / phospholipid translocation / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cellular response to dexamethasone stimulus / response to cadmium ion / lactation / response to progesterone / placenta development / cellular response to estradiol stimulus / brush border membrane / female pregnancy / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / apical plasma membrane / response to xenobiotic stimulus / 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
2,4-dibromophenyl 2,4,6-tribromophenyl ether / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsAller, S.G. / Le, C.A.
CitationJournal: Iucrj / Year: 2020
Title: Structural definition of polyspecific compensatory ligand recognition by P-glycoprotein.
Authors: Le, C.A. / Harvey, D.S. / Aller, S.G.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent translocase ABCB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,1342
Polymers141,5701
Non-polymers5651
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)90.397, 138.027, 193.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP-dependent translocase ABCB1 / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 1A / Multidrug ...ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 1A / Multidrug resistance protein 3 / P-glycoprotein 3 / Phospholipid transporter ABCB1


Mass: 141569.531 Da / Num. of mol.: 1 / Mutation: N83Q,N87Q, N90Q,F724A, C952A
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, ABC-type xenobiotic transporter, P-type phospholipid transporter
#2: Chemical ChemComp-4C8 / 2,4-dibromophenyl 2,4,6-tribromophenyl ether


Mass: 564.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H5Br5O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 71.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Hepes, lithium sulfate, EDTA, polyethylene glycol (PEG) 600 (pH 7.9 to 8.4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91963 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 36639 / % possible obs: 85.2 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Χ2: 0.541 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.1-4.492.70.813280.710.4750.9520.3693.2
4.49-4.5811.50.5318260.90.1610.5560.44496.7
4.58-4.6812.90.4888460.9410.140.5080.43199.8
4.68-4.7912.60.4338630.9590.1250.4510.43299.8
4.79-4.9112.50.3538520.9640.1030.3680.429100
4.91-5.0413.70.3478840.9730.0960.360.42599.8
5.04-5.1913.80.3088530.9790.0850.320.4499.8
5.19-5.3513.70.2848650.9840.0790.2950.43499.9
5.35-5.5413.70.2668660.9840.0740.2770.44399.9
5.54-5.7713.60.2418620.9870.0670.2510.4499.9
5.77-6.0313.30.2118810.9920.0590.2190.44799.9
6.03-6.35130.1598670.9930.0460.1660.45199.9
6.35-6.74120.138750.9950.0390.1360.46399.9
6.74-7.2612.60.0998770.9980.0290.1030.47399.9
7.26-7.9912.90.0718880.9980.020.0740.48299.9
7.99-9.1413.40.0559080.9980.0160.0580.547100
9.14-11.4912.60.0499080.9990.0140.0510.634100
11.49-5011.70.0469800.9990.0140.0481.7899.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHENIX1.14-3260-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xwk without BDE100

4xwk


Resolution: 4.1→29.81 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.57
RfactorNum. reflection% reflection
Rfree0.2946 3479 9.5 %
Rwork0.2714 --
obs0.2735 36639 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 343.22 Å2 / Biso mean: 217.5254 Å2 / Biso min: 137.22 Å2
Refinement stepCycle: final / Resolution: 4.1→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9157 0 18 0 9175
Biso mean--238.37 --
Num. residues----1182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.1-4.160.36651340.35113111445100
4.16-4.220.30271360.327413261462100
4.22-4.280.3421430.309113471490100
4.28-4.340.33331400.300113251465100
4.34-4.420.33021300.309412911421100
4.42-4.490.30541420.300713531495100
4.49-4.570.34161430.296913271470100
4.57-4.660.2641380.280113381476100
4.66-4.760.29911410.293513541495100
4.76-4.860.32461380.264312981436100
4.86-4.970.34071380.284513421480100
4.97-5.090.28331380.284913181456100
5.09-5.230.29951370.285313051442100
5.23-5.380.32831420.29513401482100
5.38-5.560.27351440.301513321476100
5.56-5.750.31051420.30213101452100
5.75-5.980.37411400.302213391479100
5.98-6.250.32751340.293513211455100
6.25-6.580.31981440.312113211465100
6.58-6.990.28311370.294113351472100
6.99-7.520.32141390.263713361475100
7.52-8.260.29671390.251213211460100
8.26-9.420.23151370.213513261463100
9.42-11.740.21591440.205913211465100
11.76-29.810.33481390.30011323146299

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