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- PDB-5kpj: Mouse pgp methylated protein -

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Basic information

Entry
Database: PDB / ID: 5kpj
TitleMouse pgp methylated protein
ComponentsMultidrug resistance protein 1A
KeywordsHYDROLASE / Mouse pgp / multidrug resistance / drug transport / methylated protein
Function / homology
Function and homology information


Atorvastatin ADME / neural tissue regeneration / aldosterone secretion / Prednisone ADME / terpenoid transport / ceramide floppase activity / phosphatidylethanolamine floppase activity / carboxylic acid transmembrane transport / regulation of chloride transport / floppase activity ...Atorvastatin ADME / neural tissue regeneration / aldosterone secretion / Prednisone ADME / terpenoid transport / ceramide floppase activity / phosphatidylethanolamine floppase activity / carboxylic acid transmembrane transport / regulation of chloride transport / floppase activity / ceramide translocation / carboxylic acid transmembrane transporter activity / ABC-family protein mediated transport / female gonad development / phosphatidylethanolamine flippase activity / cardiac muscle cell differentiation / phosphatidylcholine floppase activity / xenobiotic transport across blood-brain barrier / stem cell proliferation / adult heart development / intercellular canaliculus / export across plasma membrane / P-type phospholipid transporter / transepithelial transport / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / exploration behavior / phospholipid translocation / ABC-type xenobiotic transporter activity / xenobiotic transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / neurogenesis / transmembrane transporter activity / gene expression / G2/M transition of mitotic cell cycle / proteasomal protein catabolic process / response to toxic substance / epidermal growth factor receptor signaling pathway / heart development / 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: 3.5 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


Theoretical massNumber of molelcules
Total (without water)141,7201
Polymers141,7201
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.646, 137.170, 186.087
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: 141719.797 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The protein was methylated in the presende of AMPPNP with formaldehyd and dimethyl amino borane and subsquently purifed by size exclusion chromatography. Crysallization with 50 mM Tris 7.5, ...Details: The protein was methylated in the presende of AMPPNP with formaldehyd and dimethyl amino borane and subsquently purifed by size exclusion chromatography. Crysallization with 50 mM Tris 7.5, 100 mM NaCl and 30% PEG550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.89 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 28399 / % possible obs: 94.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 109.56 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.048 / Rrim(I) all: 0.144 / Χ2: 1.005 / Net I/av σ(I): 8.686 / Net I/σ(I): 7.9 / Num. measured all: 177435
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.633.20.45725140.0810.2690.5350.40184.9
3.63-3.773.40.61826130.1060.3940.7371.27288.7
3.77-3.943.70.46726770.1120.2570.5370.64890.8
3.94-4.154.10.42827450.150.2220.4860.50492.6
4.15-4.4150.36828200.5280.1670.4070.63195.4
4.41-4.756.30.29829130.8230.1180.3220.95296.9
4.75-5.237.20.24729290.9180.0910.2651.15298.4
5.23-5.987.80.21129790.9640.0760.2251.19298.6
5.98-7.539.30.15530450.9870.050.1631.0799.5
7.53-5010.80.11231640.9850.0360.1181.18299.1

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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: 3.5→21.451 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 40.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3149 1355 4.96 %
Rwork0.2855 --
obs0.287 27306 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→21.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9137 0 0 2 9139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059306
X-RAY DIFFRACTIONf_angle_d1.07812584
X-RAY DIFFRACTIONf_dihedral_angle_d13.4595546
X-RAY DIFFRACTIONf_chiral_restr0.0581448
X-RAY DIFFRACTIONf_plane_restr0.0081597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.62460.4191040.38682161X-RAY DIFFRACTION79
3.6246-3.7690.43671180.40662382X-RAY DIFFRACTION88
3.769-3.93950.40131390.38862440X-RAY DIFFRACTION89
3.9395-4.14580.36641300.3542532X-RAY DIFFRACTION92
4.1458-4.40350.32681180.31042621X-RAY DIFFRACTION95
4.4035-4.74010.3261530.27162633X-RAY DIFFRACTION97
4.7401-5.21090.29961470.25832720X-RAY DIFFRACTION98
5.2109-5.95080.29821420.28472742X-RAY DIFFRACTION99
5.9508-7.4450.33531390.30842818X-RAY DIFFRACTION99
7.445-21.45150.26611650.22662902X-RAY DIFFRACTION100

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