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- PDB-6ujn: P-glycoprotein mutant-C952A-with BDE100 -

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Basic information

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


hormone transport / cellular response to nonylphenol / 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 ...hormone transport / cellular response to nonylphenol / 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 / positive regulation of establishment of Sertoli cell barrier / regulation of intestinal absorption / response to quercetin / cellular response to external biotic stimulus / response to antineoplastic agent / Prednisone ADME / terpenoid transport / ceramide floppase activity / establishment of blood-retinal barrier / response to glycoside / protein localization to bicellular tight junction / ceramide translocation / floppase activity / ABC-family proteins mediated transport / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / cellular response to L-glutamate / xenobiotic transport across blood-brain barrier / intercellular canaliculus / xenobiotic detoxification by transmembrane export across the plasma membrane / response to vitamin D / export across plasma membrane / P-type phospholipid transporter / ABC-type xenobiotic transporter / response to alcohol / response to vitamin A / response to glucagon / intestinal absorption / ABC-type xenobiotic transporter activity / cellular response to antibiotic / phospholipid translocation / cellular hyperosmotic salinity response / cellular response to alkaloid / maintenance of blood-brain barrier / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / response to progesterone / female pregnancy / placenta development / cellular response to estradiol stimulus / brush border membrane / 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: 3.98 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)142,2102
Polymers141,6461
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)87.570, 137.543, 184.507
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: 141645.625 Da / Num. of mol.: 1 / Mutation: N83Q,N87Q, N90Q,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: 3.99 Å3/Da / Density % sol: 69.16 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Hepes, lithium sulfate, EDTA, and 26-28.5% (w/v) 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: 0.91959 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91959 Å / Relative weight: 1
ReflectionResolution: 3.98→50 Å / Num. obs: 36876 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Χ2: 0.523 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.98-4.0512.31.2529440.7080.3681.3070.41999.9
4.05-4.1212.60.989840.7870.2851.0210.428100
4.12-4.212.80.8419620.8380.2430.8760.429100
4.2-4.2912.90.6259700.9050.180.6510.424100
4.29-4.3812.80.5349850.9230.1550.5560.436100
4.38-4.4812.20.4189540.9510.1240.4370.44100
4.48-4.5913.40.3679930.9640.1040.3820.456100
4.59-4.7213.40.3179610.9720.090.330.449100
4.72-4.8613.10.2679820.9790.0760.2780.465100
4.86-5.0112.70.2389660.9840.0690.2480.451100
5.01-5.1913.90.2159940.9890.060.2240.464100
5.19-5.413.80.219640.9910.0580.2180.472100
5.4-5.6513.60.1919900.9920.0540.1990.457100
5.65-5.9413.40.1779980.9950.050.1840.476100
5.94-6.3112.90.13510010.9950.0390.1410.485100
6.31-6.812.60.1039970.9970.030.1080.496100
6.8-7.4812.70.0779930.9980.0220.080.521100
7.48-8.5613.20.05410250.9990.0150.0560.592100
8.56-10.7712.80.04110310.9990.0120.0430.694100
10.77-5011.50.04110980.9990.0130.0431.398100

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Processing

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

4xwk


Resolution: 3.98→29.95 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 3123 8.49 %
Rwork0.2429 33649 -
obs0.2448 36772 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 312.21 Å2 / Biso mean: 190.8707 Å2 / Biso min: 113.48 Å2
Refinement stepCycle: final / Resolution: 3.98→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9163 0 18 0 9181
Biso mean--208.66 --
Num. residues----1182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.98-4.040.30741390.312115081647100
4.04-4.110.32071420.310515321674100
4.11-4.180.30381500.299115731723100
4.18-4.250.31181400.289114881628100
4.26-4.340.27441460.27415231669100
4.34-4.420.33291400.274915581698100
4.42-4.520.30291410.266415011642100
4.52-4.630.28011400.262315551695100
4.63-4.740.26221400.254815261666100
4.74-4.870.23341410.250515381679100
4.87-5.010.32931370.24915041641100
5.01-5.170.29591460.245515421688100
5.17-5.360.33531450.262115421687100
5.36-5.570.35121440.289815191663100
5.57-5.820.37311470.281415481695100
5.82-6.120.25441390.28314991638100
6.13-6.50.28311470.26315341681100
6.51-70.25511340.240615311665100
7-7.70.27631450.223915501695100
7.7-8.780.22111390.197315461685100
8.79-10.980.1791430.17915191662100
10.98-29.950.26411380.25581513165199

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