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- PDB-5kpi: Mouse native PGP -

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Basic information

Entry
Database: PDB / ID: 5kpi
TitleMouse native PGP
ComponentsMultidrug resistance protein 1A
KeywordsHYDROLASE / Mouse pgp / multidrug resistance / drug transport / native
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 / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / ceramide translocation / establishment of blood-retinal barrier / protein localization to bicellular tight junction / cellular response to L-glutamate / 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 / 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 / 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
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
ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 Å
AuthorsXia, D. / Esser, L. / Zhou, F.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity.
Authors: Esser, L. / Zhou, F. / Pluchino, K.M. / Shiloach, J. / Ma, J. / Tang, W.K. / Gutierrez, C. / Zhang, A. / Shukla, S. / Madigan, J.P. / Zhou, T. / Kwong, P.D. / Ambudkar, S.V. / Gottesman, M.M. / Xia, D.
History
DepositionJul 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance protein 1A
B: Multidrug resistance protein 1A


Theoretical massNumber of molelcules
Total (without water)283,2712
Polymers283,2712
Non-polymers00
Water00
1
A: Multidrug resistance protein 1A


Theoretical massNumber of molelcules
Total (without water)141,6361
Polymers141,6361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multidrug resistance protein 1A


Theoretical massNumber of molelcules
Total (without water)141,6361
Polymers141,6361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.607, 119.535, 383.887
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 / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 3 / P-glycoprotein 3


Mass: 141635.609 Da / Num. of mol.: 2
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 GS115 (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase

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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: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 50 mM Glycine9.0 100 mM NaCl, 22-24% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→35.405 Å / Num. obs: 37665 / % possible obs: 95.3 % / Redundancy: 5 % / Biso Wilson estimate: 186.57 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.035 / Rrim(I) all: 0.08 / Χ2: 0.999 / Net I/av σ(I): 16.956 / Net I/σ(I): 7.6 / Num. measured all: 187287
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
4-4.1240.8550.452182
4.12-4.254.30.6740.677186.7
4.25-4.44.50.520.839190.6
4.4-4.584.70.3890.896193.7
4.58-4.794.90.3190.936196.9
4.79-5.045.10.2750.96199.9
5.04-5.355.30.240.9661100
5.35-5.775.30.2050.975199.9
5.77-6.355.40.1560.985199.9
6.35-7.265.40.0950.993199.8
7.26-9.145.40.0530.998199.4
9.14-504.90.0360.999194.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2443: ???)refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M1M

4m1m


Resolution: 4.01→20.138 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3026 1860 4.98 %
Rwork0.2576 --
obs0.2599 37361 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.01→20.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18374 0 0 0 18374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718712
X-RAY DIFFRACTIONf_angle_d1.02325295
X-RAY DIFFRACTIONf_dihedral_angle_d12.57311163
X-RAY DIFFRACTIONf_chiral_restr0.0552914
X-RAY DIFFRACTIONf_plane_restr0.0083215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0097-4.11720.3941250.36162040X-RAY DIFFRACTION73
4.1172-4.23730.35631350.33642448X-RAY DIFFRACTION87
4.2373-4.37270.34461350.312530X-RAY DIFFRACTION89
4.3727-4.52730.33791130.26672651X-RAY DIFFRACTION93
4.5273-4.70640.24871440.24812694X-RAY DIFFRACTION95
4.7064-4.91760.27391370.24462815X-RAY DIFFRACTION98
4.9176-5.17270.29441560.24962866X-RAY DIFFRACTION100
5.1727-5.49060.2971450.27012852X-RAY DIFFRACTION100
5.4906-5.90460.38911370.29462912X-RAY DIFFRACTION100
5.9046-6.48080.36481610.29752882X-RAY DIFFRACTION100
6.4808-7.37790.33791620.27582901X-RAY DIFFRACTION100
7.3779-9.1480.25391360.23852956X-RAY DIFFRACTION99
9.148-20.13850.28441740.23162954X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.88240.95911.06880.93-0.66920.13290.17990.1946-0.5377-1.0840.2689-0.209-0.60890.3285-0.35622.0775-0.24730.24571.5451-0.31111.872528.969167.656411.7442
21.74261.2090.66141.15380.80351.16070.347-0.0922-0.3854-0.3643-0.3399-0.0589-0.14640.17810.03851.9671-0.05040.05251.3847-0.11761.504439.786391.379341.9776
3-0.0181-0.5531-0.24920.6614-0.4712-0.31920.16610.2758-0.2638-0.6135-0.48040.41330.1487-0.32990.28352.291-0.3038-0.00611.8488-0.46862.150612.833764.169518.4369
40.5815-0.68911.6014-0.25020.23131.9830.3859-0.64790.3756-0.05670.3781.1171-1.3947-0.4009-0.42412.4804-0.07930.40642.0968-0.69792.2734-1.7611102.901353.7769
54.38854.9549-4.59542.9021-3.74732.09670.0809-1.08270.01670.20190.24560.446-0.44550.2398-0.10361.54010.08970.22352.64650.22982.022428.489956.089885.8613
60.5368-3.4665-0.7046-4.29581.4482-1.1063-1.1585-0.1178-0.77360.8751.0491.69180.6238-0.0396-0.20551.9821-0.35390.44142.98720.31842.819341.205132.887386.034
76.5467-1.25782.2332.93452.39575.7256-0.4086-0.58160.8135-0.80510.2864-0.5697-1.3589-0.06590.08041.0964-0.2290.3941.4960.0821.39272.142966.347648.3165
82.38571.0036-1.25031.8412-0.86561.2991-0.24370.0141-0.39530.02870.33720.34210.196-0.5546-0.05341.4164-0.4085-0.11381.76660.1671.515638.651938.685671.0146
95.0862-1.7603-1.52280.86030.04770.3472-0.4515-0.9420.184-0.42940.5836-0.41380.15490.9323-0.11482.2027-0.47130.39342.8222-0.23261.889864.949419.078653.7213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 278 )
2X-RAY DIFFRACTION2chain 'A' and (resid 279 through 692 )
3X-RAY DIFFRACTION3chain 'A' and (resid 693 through 1029 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1030 through 1272 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 217 )
6X-RAY DIFFRACTION6chain 'B' and (resid 218 through 366 )
7X-RAY DIFFRACTION7chain 'B' and (resid 367 through 589 )
8X-RAY DIFFRACTION8chain 'B' and (resid 590 through 953 )
9X-RAY DIFFRACTION9chain 'B' and (resid 954 through 1271 )

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