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- PDB-5ko2: Mouse pgp 34 linker deleted mutant Hg derivative -

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Basic information

Entry
Database: PDB / ID: 5ko2
TitleMouse pgp 34 linker deleted mutant Hg derivative
ComponentsMultidrug resistance protein 1A
KeywordsHYDROLASE / Mouse pgp / multidrug resistance / drug transport / Mercury derivative
Function / homology
Function and homology information


Atorvastatin ADME / aldosterone secretion / Prednisone ADME / neural tissue regeneration / cellular response to nonylphenol / cellular response to borneol / response to codeine / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug ...Atorvastatin ADME / aldosterone secretion / Prednisone ADME / neural tissue regeneration / cellular response to nonylphenol / cellular response to borneol / response to codeine / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / terpenoid transport / ceramide floppase activity / regulation of intestinal absorption / cellular response to external biotic stimulus / response to cyclosporin A / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / negative regulation of sensory perception of pain / carboxylic acid transmembrane transport / floppase activity / ceramide translocation / ABC-family proteins mediated transport / response to quercetin / carboxylic acid transmembrane transporter activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / xenobiotic transport across blood-brain barrier / response to thyroxine / intercellular canaliculus / establishment of blood-brain barrier / export across plasma membrane / cardiac muscle cell differentiation / xenobiotic detoxification by transmembrane export across the plasma membrane / P-type phospholipid transporter / transepithelial transport / cellular response to L-glutamate / ABC-type xenobiotic transporter / adult heart development / response to vitamin A / response to vitamin D / response to glucagon / intestinal absorption / response to glycoside / response to alcohol / ABC-type xenobiotic transporter activity / phospholipid translocation / cellular hyperosmotic salinity response / cellular response to alkaloid / female gonad development / maintenance of blood-brain barrier / cellular response to antibiotic / exploration behavior / ATPase-coupled transmembrane transporter activity / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / cellular response to dexamethasone stimulus / transmembrane transporter activity / response to cadmium ion / xenobiotic transport / lactation / response to progesterone / proteasomal protein catabolic process / neurogenesis / regulation of chloride transport / placenta development / stem cell proliferation / cellular response to estradiol stimulus / brush border membrane / female pregnancy / circadian rhythm / G2/M transition of mitotic cell cycle / response to toxic substance / cellular response to tumor necrosis factor / epidermal growth factor receptor signaling pathway / heart development / cellular response to lipopolysaccharide / gene expression / response to hypoxia / apical plasma membrane / response to xenobiotic stimulus / ubiquitin protein ligase binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 3.3 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
DepositionJun 29, 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 1.3Sep 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,39516
Polymers275,5872
Non-polymers2,80814
Water00
1
A: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1978
Polymers137,7931
Non-polymers1,4047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1978
Polymers137,7931
Non-polymers1,4047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.185, 114.741, 375.431
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
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: P21447, EC: 3.6.3.44
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 14 / 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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein is pre-incubated with p-chloromercury phenylsulfonate to a final concentration of 4 mM of the organo mercury compound. To 10.5 ul of protein/organomercury, 3.5 ul of the precipitant ...Details: Protein is pre-incubated with p-chloromercury phenylsulfonate to a final concentration of 4 mM of the organo mercury compound. To 10.5 ul of protein/organomercury, 3.5 ul of the precipitant 25 mM HEPES 7.5 pH, 100 mM NaCl, 0.3 mM Cymal -7, 28% PEG400 was added. Reservoir: 50 mM HEPES 7.5pH, 100 mM NaCl 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 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.109 Å / Num. obs: 114118 / % possible obs: 92.2 % / Redundancy: 11.5 % / Biso Wilson estimate: 114.81 Å2 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.042 / Rrim(I) all: 0.154 / Χ2: 0.991 / Net I/av σ(I): 13.443 / Net I/σ(I): 9 / Num. measured all: 1309474
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.3-3.388.30.9680.217189.4
3.38-3.469.20.9050.302190.5
3.46-3.559.80.8290.474191.1
3.55-3.6610.30.6940.67191.4
3.66-3.7810.70.60.78191.4
3.78-3.91110.4790.886192
3.91-4.0711.30.3720.939191.8
4.07-4.2511.70.2820.967191.7
4.25-4.4812.10.2190.982192
4.48-4.7612.40.1750.988192
4.76-5.1312.50.1580.99191.7
5.13-5.6412.60.1490.99192
5.64-6.4612.80.1410.991192.4
6.46-8.13130.1060.996196.1
8.13-5014.10.1040.994197.6

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Processing

Software
NameVersionClassification
PHENIXdev_2443refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M1M

4m1m


Resolution: 3.3→33.536 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 3756 3.31 %Random
Rwork0.243 ---
obs0.2444 113533 92.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→33.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18374 0 14 0 18388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518732
X-RAY DIFFRACTIONf_angle_d0.66425295
X-RAY DIFFRACTIONf_dihedral_angle_d15.5296807
X-RAY DIFFRACTIONf_chiral_restr0.0522914
X-RAY DIFFRACTIONf_plane_restr0.0043215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.34170.36691320.35893839X-RAY DIFFRACTION87
3.3417-3.38570.34811330.35783997X-RAY DIFFRACTION90
3.3857-3.4320.42581360.35333970X-RAY DIFFRACTION91
3.432-3.4810.35451370.35293988X-RAY DIFFRACTION90
3.481-3.53290.36211380.33934037X-RAY DIFFRACTION92
3.5329-3.5880.35441360.3263990X-RAY DIFFRACTION90
3.588-3.64680.34931430.33084054X-RAY DIFFRACTION92
3.6468-3.70960.38061320.30524000X-RAY DIFFRACTION91
3.7096-3.7770.321430.30534124X-RAY DIFFRACTION92
3.777-3.84950.36631350.29444020X-RAY DIFFRACTION92
3.8495-3.9280.31571350.28594094X-RAY DIFFRACTION92
3.928-4.01320.27871340.27823972X-RAY DIFFRACTION92
4.0132-4.10640.27891370.25774103X-RAY DIFFRACTION92
4.1064-4.2090.24421390.24974037X-RAY DIFFRACTION92
4.209-4.32250.2731430.2384030X-RAY DIFFRACTION92
4.3225-4.44940.24271400.22564100X-RAY DIFFRACTION92
4.4494-4.59270.23521390.20684029X-RAY DIFFRACTION92
4.5927-4.75640.21781390.2044037X-RAY DIFFRACTION93
4.7564-4.94630.20951380.20464087X-RAY DIFFRACTION92
4.9463-5.17060.24751390.2144074X-RAY DIFFRACTION92
5.1706-5.44220.3161340.22944015X-RAY DIFFRACTION92
5.4422-5.78150.31691420.24974095X-RAY DIFFRACTION92
5.7815-6.22530.27421380.24984022X-RAY DIFFRACTION93
6.2253-6.84690.27031430.23384156X-RAY DIFFRACTION94
6.8469-7.82670.27391440.22284266X-RAY DIFFRACTION97
7.8267-9.81960.22531560.18154310X-RAY DIFFRACTION98
9.8196-33.53750.31771510.23574331X-RAY DIFFRACTION99
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)
10.77180.2898-0.24483.5521.04631.76680.24010.24180.0176-1.0538-0.30230.66270.15360.1306-0.25551.06270.0669-0.17080.4916-0.38030.980236.246851.90325.5074
22.66470.2857-0.46651.7130.9831.27690.25360.18810.5281-0.59970.0856-0.0253-0.6734-0.1555-0.30081.246-0.12540.01650.72130.07040.876819.792274.12839.6599
31.33461.2780.92973.01932.1411.53070.1653-0.11770.0904-0.11620.1054-0.128-0.45130.1479-0.27971.2114-0.02130.04380.885-0.23211.106344.454488.518444.5204
41.34360.48440.15420.19460.19180.68540.0277-0.06130.18210.2182-0.19460.23180.1578-0.2150.15070.7707-0.1234-0.00840.4655-0.10240.939719.999969.240123.61
50.38190.41970.07940.22130.0263-0.08010.0071-0.5002-0.41770.17030.20050.40740.39810.4637-0.2321.1886-0.11590.23361.044-0.29311.12571.31792.042646.3151
66.04762.9099-3.10271.1092-1.68392.03440.5001-0.71090.66580.31640.05680.331-0.54970.2487-0.6450.82760.09520.27811.28840.03291.12120.876255.707384.3237
71.30930.2645-0.86770.6186-0.49681.5075-0.0675-0.06810.0690.00210.1134-0.05360.24470.0886-0.05240.8885-0.03680.1651.1081-0.01660.870552.732647.97274.3532
86.5087-1.64271.59824.78460.2435.8379-0.39161.1214-0.6492-0.49490.38310.105-0.53110.3669-0.04460.56070.06260.19020.7655-0.07390.723464.93362.249437.424
90.6258-0.522-0.10661.4943-0.30990.8251-0.17680.0023-0.2962-0.20080.1447-0.12770.2661-0.0412-0.02250.9132-0.15810.04540.9372-0.12930.837437.954238.307868.8125
103.5256-1.0733-1.41111.51280.25930.7780.1529-0.73110.7308-0.40070.1622-0.2346-0.16090.6194-0.33011.0217-0.28360.24551.3698-0.2090.92766.941219.287652.1522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 323 )
3X-RAY DIFFRACTION3chain 'A' and (resid 324 through 572 )
4X-RAY DIFFRACTION4chain 'A' and (resid 573 through 961 )
5X-RAY DIFFRACTION5chain 'A' and (resid 962 through 1272 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 153 )
7X-RAY DIFFRACTION7chain 'B' and (resid 154 through 479 )
8X-RAY DIFFRACTION8chain 'B' and (resid 480 through 581 )
9X-RAY DIFFRACTION9chain 'B' and (resid 582 through 961 )
10X-RAY DIFFRACTION10chain 'B' and (resid 962 through 1271 )

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