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- PDB-5kpd: Mouse pgp 34 linker deleted double EQ mutant -

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Basic information

Entry
Database: PDB / ID: 5kpd
TitleMouse pgp 34 linker deleted double EQ mutant
ComponentsMultidrug resistance protein 1A
KeywordsHYDROLASE / multidrug resistance / ABC transporter / membrane protein / drug efflux
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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.35 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 3, 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: Data collection / 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)275,5872
Polymers275,5872
Non-polymers00
Water00
1
A: Multidrug resistance protein 1A


Theoretical massNumber of molelcules
Total (without water)137,7931
Polymers137,7931
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multidrug resistance protein 1A


Theoretical massNumber of molelcules
Total (without water)137,7931
Polymers137,7931
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.953, 116.594, 375.557
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: 137793.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: From original mouse PGP the linker the following protion was deleted: 649-682 ms skdsgsslir rrstrksicg phdqdrklst ke Also Walker B sequence was mutated. The sequence numbering of the orginal ...Details: From original mouse PGP the linker the following protion was deleted: 649-682 ms skdsgsslir rrstrksicg phdqdrklst ke Also Walker B sequence was mutated. The sequence numbering of the orginal mouse pgp was maintained (despite the 2nd have being shifted by 34). Thus resiues 552 and 1197 which are E were mutated to Q to make the ATP site inactive.
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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: In the setup the rotein at 10.6 mg of 4 ul volume was diluted with 0.2 ul water and treated with 4 ul of 28% PEG400, 50 mM Glycine 9.0 and 100 mM NaCl. The reservoir solution conatined 100 ...Details: In the setup the rotein at 10.6 mg of 4 ul volume was diluted with 0.2 ul water and treated with 4 ul of 28% PEG400, 50 mM Glycine 9.0 and 100 mM NaCl. The reservoir solution conatined 100 mM Glycine 9.0pH, 150 mM NaCl, 10 mM NaN3 and 30% 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: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→29.944 Å / Num. obs: 62273 / % possible obs: 96.5 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.101 / Net I/av σ(I): 1.1 / Net I/σ(I): 17.5
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.463

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Processing

Software
NameVersionClassification
PHENIXdev_2443refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KO2

5ko2


Resolution: 3.35→22.416 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 34.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 2337 4.02 %
Rwork0.24 --
obs0.2417 58196 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→22.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18374 0 0 0 18374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818712
X-RAY DIFFRACTIONf_angle_d1.20825295
X-RAY DIFFRACTIONf_dihedral_angle_d12.86511163
X-RAY DIFFRACTIONf_chiral_restr0.0642914
X-RAY DIFFRACTIONf_plane_restr0.0073215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.41820.38251180.38222643X-RAY DIFFRACTION77
3.4182-3.49220.43831130.39282817X-RAY DIFFRACTION81
3.4922-3.57310.40461270.39312864X-RAY DIFFRACTION83
3.5731-3.66210.39841360.38312959X-RAY DIFFRACTION85
3.6621-3.76070.43291480.37143110X-RAY DIFFRACTION89
3.7607-3.87080.36771190.33693053X-RAY DIFFRACTION87
3.8708-3.99510.34441290.31863206X-RAY DIFFRACTION91
3.9951-4.1370.30811190.28283326X-RAY DIFFRACTION95
4.137-4.30150.31561310.25013414X-RAY DIFFRACTION97
4.3015-4.49580.2271740.22443423X-RAY DIFFRACTION98
4.4958-4.73070.25341410.20213481X-RAY DIFFRACTION99
4.7307-5.0240.24461580.20163483X-RAY DIFFRACTION99
5.024-5.40690.23721510.20623542X-RAY DIFFRACTION99
5.4069-5.94180.26181420.23563545X-RAY DIFFRACTION100
5.9418-6.78070.28911280.24023599X-RAY DIFFRACTION100
6.7807-8.46570.29051480.21793647X-RAY DIFFRACTION100
8.4657-22.41630.23941550.19393747X-RAY DIFFRACTION100
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)
10.23-0.19610.3292.3631-1.43632.050.3213-0.19590.0843-0.0048-0.99960.1909-0.0966-0.3873-0.06241.14-0.00820.48440.9327-0.61741.284640.221560.33535.9364
20.31810.1260.56950.75141.60484.01260.4103-0.01931.53290.18610.42810.64750.4242-1.06440.44931.9983-0.81541.07471.6183-0.38852.749120.322825.6687-17.9264
32.223-0.5839-1.31040.7443-0.32641.4322-0.12040.0083-0.4568-0.42610.196-0.22230.0160.5799-0.10030.8335-0.18490.16920.6851-0.11690.816438.939864.591515.5174
42.6139-0.0064-0.10942.72511.53262.0386-0.2497-0.22550.47860.3130.8386-0.0161-0.40290.57970.92432.188-0.7335-0.00810.96-0.10520.493123.651670.1732-6.5089
51.0896-1.4425-1.74064.47074.4144.31960.79860.3597-0.0219-1.9515-0.4358-0.2058-1.734-0.7406-0.36561.6334-0.12410.1521.06910.01081.219410.009976.57449.3755
60.67260.7030.41592.24582.73212.98530.6731-0.0649-0.21090.0736-0.1863-0.6735-0.0502-0.3338-0.14551.7384-0.02470.15871.0704-0.22951.243745.582292.110131.0291
72.54521.27530.04444.9006-0.6334.26720.2392-0.2252-0.59920.0384-0.0092-0.461-0.41140.8048-0.13971.2977-0.19470.05661.0024-0.27440.990545.725690.914256.2453
80.8444-0.1958-0.2950.27290.03041.5231-0.4861-0.17390.3711-0.3924-0.16950.5495-0.2242-0.45170.36790.79810.0516-0.11260.6197-0.15031.011122.134988.907635.4797
91.98941.0312-1.22983.4804-0.09980.8563-0.34311.2241-0.226-1.2611-0.68961.7635-0.9643-0.56340.42421.47750.049-0.35321.2238-0.40711.02239.435955.3454-11.9466
101.4332-1.11730.38621.8451.2152.592-0.32770.2594-0.2976-0.31480.61160.29330.13710.4242-0.14811.0515-0.18490.16060.694-0.07331.23119.777364.560221.0773
110.92130.46760.7411.23280.39363.3961-0.1340.44640.27430.5805-0.27290.53030.62160.12960.30460.6432-0.10360.26670.799-0.00881.096436.760162.110226.5597
120.8263-1.04880.05524.04143.74365.17020.04750.3085-0.5837-0.44070.8575-0.4224-0.44081.0772-0.39361.171-0.29530.00891.3054-0.38711.29249.281360.111216.6363
132.69190.22010.90921.1163-0.65551.91440.0207-0.695-0.82490.1856-0.02680.2164-0.36140.0017-0.04821.1944-0.07240.32721.1491-0.49271.3139-3.696993.864752.4569
141.6955-0.1853-0.26231.9076-0.13720.04780.6616-0.76280.33950.84080.01040.51190.38430.14520.63811.2519-0.11390.4060.3428-0.56121.38723.2217111.407444.1514
154.74843.50141.25995.1934-0.1160.7521-0.70051.3417-0.9803-1.3831.1581-0.48330.01520.61930.78531.5369-1.00590.64211.7651-0.71491.56949.6014107.726562.8642
160.71331.89120.46025.90860.11621.570.3481-0.8671.0025-0.9265-0.63321.5547-0.61790.22760.42031.5027-0.35940.63091.2926-0.65651.3616.9077102.571372.011
172.4890.8106-1.25540.7398-1.49443.88691.1310.34640.40691.1252-0.5858-0.6901-1.1496-0.1593-0.27330.9938-0.09650.20850.7117-0.32551.284727.041258.456787.2368
186.77732.7871-4.18581.8281-1.00372.5920.10780.26470.56640.07430.15570.0036-0.2061-0.2137-0.09160.83790.12210.00340.78750.09370.851827.664856.824878.4992
192.55931.28030.29763.2911-2.85323.70280.3218-0.5480.03030.61480.4209-0.38391.2812-2.0221-0.41411.0961-0.26740.07981.48770.08661.110929.60748.747695.1653
205.5341-4.0752-5.12562.76583.284.97890.0237-1.78860.4499-0.11421.46580.2399-1.3341.3542-0.38891.3491-0.03260.14551.53070.01331.40249.621722.9676.9349
211.50230.9828-0.11080.7573-0.07551.834-0.1831-0.002-0.94320.3086-0.0488-0.2971-0.15480.42780.25110.65250.05750.12271.33720.19141.232828.884848.106193.1527
221.38331.7697-0.22363.38850.59443.70310.0069-0.6843-0.0457-0.0634-0.101-0.3398-0.42320.0930.04120.83670.00820.38231.2649-0.0461.190973.417267.922151.9304
233.9806-0.99241.82282.17511.60243.3521-0.3187-0.04410.0355-0.2487-0.09320.45570.1119-0.70260.1510.8906-0.14760.31391.00960.02861.145969.26160.686838.5961
241.0364-0.18870.40063.4628-1.04880.386-0.56790.17070.3869-0.0995-0.5116-1.56390.0017-0.1737-0.1751.3830.25170.4751.834-0.23221.241285.838953.482645.0043
251.448-1.2286-0.7291.22530.13040.98030.2895-0.5436-0.31180.24220.7601-0.29480.0370.24521.25250.6033-0.74660.26530.9151-0.18021.658419.180824.377484.4546
262.24040.8452-0.18150.40550.08280.61980.263-0.66240.06561.0736-0.12531.0265-0.1527-0.5397-3.22341.085-0.26820.5740.75091.13541.174715.198727.0969100.5126
271.6506-1.3595-1.68671.37691.1571.7446-0.450.8109-0.6029-0.20550.29640.31030.0218-0.51730.0941.08180.01280.03841.16870.07561.336232.238329.920870.0849
283.7236-0.3885-2.266-0.04190.08161.5836-0.5091.1679-1.54980.11210.1853-0.40180.1905-1.08360.18430.8236-0.14310.10071.30220.12631.28628.071853.227570.6898
292.9967-0.4626-0.79391.65530.5410.6767-0.37250.5041-1.0045-0.8869-0.07540.8860.1272-0.38990.20491.4199-0.25410.18331.483-0.11441.259563.455918.585647.5074
306.9343-1.84893.691.6388-3.23326.3814-1.0145-2.50591.12310.0411-1.2811-0.00430.14281.6018-0.31511.3010.56730.11533.3353-0.90731.73983.500810.244166.606
311.87390.12530.70672.37370.79814.1112-0.1502-0.8187-1.2779-0.5886-0.3381-0.2166-0.2379-0.72890.17541.3686-0.46980.01781.71580.35651.103177.563818.600260.3048
321.8187-0.7851-0.11721.64860.13120.15540.20710.4727-0.3245-0.6694-0.2894-0.89430.59050.01420.08921.4271-0.39640.6642.0916-0.30571.094286.454124.904941.2475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 28:81)
2X-RAY DIFFRACTION2(chain A and resid 82:99)
3X-RAY DIFFRACTION3(chain A and resid 100:203)
4X-RAY DIFFRACTION4(chain A and resid 204:237)
5X-RAY DIFFRACTION5(chain A and resid 238:327)
6X-RAY DIFFRACTION6(chain A and resid 328:431)
7X-RAY DIFFRACTION7(chain A and resid 432:581)
8X-RAY DIFFRACTION8(chain A and resid 582:731)
9X-RAY DIFFRACTION9(chain A and resid 732:771)
10X-RAY DIFFRACTION10(chain A and resid 772:883)
11X-RAY DIFFRACTION11(chain A and resid 884:962)
12X-RAY DIFFRACTION12(chain A and resid 963:1017)
13X-RAY DIFFRACTION13(chain A and resid 1018:1136)
14X-RAY DIFFRACTION14(chain A and resid 1137:1226)
15X-RAY DIFFRACTION15(chain A and resid 1227:1234)
16X-RAY DIFFRACTION16(chain A and resid 1235:1272)
17X-RAY DIFFRACTION17(chain B and resid 28:84)
18X-RAY DIFFRACTION18(chain B and resid 85:178)
19X-RAY DIFFRACTION19(chain B and resid 179:230)
20X-RAY DIFFRACTION20(chain B and resid 231:306)
21X-RAY DIFFRACTION21(chain B and resid 307:366)
22X-RAY DIFFRACTION22(chain B and resid 367:510)
23X-RAY DIFFRACTION23(chain B and resid 511:585)
24X-RAY DIFFRACTION24(chain B and resid 586:693)
25X-RAY DIFFRACTION25(chain B and resid 694:743)
26X-RAY DIFFRACTION26(chain B and resid 744:763)
27X-RAY DIFFRACTION27(chain B and resid 764:883)
28X-RAY DIFFRACTION28(chain B and resid 884:989)
29X-RAY DIFFRACTION29(chain B and resid 990:1135)
30X-RAY DIFFRACTION30(chain B and resid 1136:1161)
31X-RAY DIFFRACTION31(chain B and resid 1162:1198)
32X-RAY DIFFRACTION32(chain B and resid 1199:1271)

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