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- PDB-4lsg: Structure of Mouse P-Glycoprotein -

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Basic information

Entry
Database: PDB / ID: 4lsg
TitleStructure of Mouse P-Glycoprotein
ComponentsMultidrug resistance protein 1A
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / ABC transporter / multidrug resistance / ATP binding / drugs
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 / ABC-type xenobiotic transporter / response to vitamin D / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 3.8 Å
AuthorsChang, G. / Szewczyk, P.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Other
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)286,09914
Polymers283,6922
Non-polymers2,40712
Water00
1
A: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0497
Polymers141,8461
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0497
Polymers141,8461
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-238 kcal/mol
Surface area108740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.542, 115.426, 378.858
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: 141845.812 Da / Num. of mol.: 2 / Mutation: 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, xenobiotic-transporting ATPase
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 12 / 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: 3.76 Å3/Da / Density % sol: 67.28 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17% PEG 350mme, 0.05M tris, 0.04% sodium cholate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.00695, 1.00923
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Dec 16, 2007
RadiationMonochromator: APS mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.006951
21.009231
ReflectionResolution: 3.8→50 Å / Num. all: 42800 / Num. obs: 41131 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.8→4.04 Å / % possible all: 86.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KSB

4ksb


Resolution: 3.8→19.983 Å / SU ML: 0.77 / σ(F): 0.01 / Phase error: 42.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3569 4203 10.22 %10.22% random
Rwork0.3356 ---
all0.3378 42800 --
obs0.3378 41118 96.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18340 0 12 0 18352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618678
X-RAY DIFFRACTIONf_angle_d1.30925254
X-RAY DIFFRACTIONf_dihedral_angle_d13.7246788
X-RAY DIFFRACTIONf_chiral_restr0.0532912
X-RAY DIFFRACTIONf_plane_restr0.0063212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.84290.45491230.42851068X-RAY DIFFRACTION84
3.8429-3.88780.50171510.46851227X-RAY DIFFRACTION97
3.8878-3.93480.55071140.4296956X-RAY DIFFRACTION78
3.9348-3.98430.48891190.43321058X-RAY DIFFRACTION81
3.9843-4.03630.39291290.40191162X-RAY DIFFRACTION94
4.0363-4.09110.44141220.39371231X-RAY DIFFRACTION96
4.0911-4.1490.45221300.40791196X-RAY DIFFRACTION95
4.149-4.21040.42951430.38771228X-RAY DIFFRACTION96
4.2104-4.27560.43061210.37641235X-RAY DIFFRACTION96
4.2756-4.3450.38581380.391194X-RAY DIFFRACTION97
4.345-4.41910.40681400.35421248X-RAY DIFFRACTION97
4.4191-4.49850.39081350.371246X-RAY DIFFRACTION98
4.4985-4.58410.39091480.34171241X-RAY DIFFRACTION97
4.5841-4.67650.41811340.35511213X-RAY DIFFRACTION96
4.6765-4.77680.3821460.36381225X-RAY DIFFRACTION97
4.7768-4.88630.39131390.36391262X-RAY DIFFRACTION98
4.8863-5.00670.37261370.34291236X-RAY DIFFRACTION98
5.0067-5.13980.39761470.35831222X-RAY DIFFRACTION97
5.1398-5.28830.42391470.36981252X-RAY DIFFRACTION98
5.2883-5.45570.39711460.36661253X-RAY DIFFRACTION99
5.4557-5.64640.44881530.37611255X-RAY DIFFRACTION99
5.6464-5.8670.39241570.38341251X-RAY DIFFRACTION99
5.867-6.12670.35271360.35571301X-RAY DIFFRACTION99
6.1267-6.43940.36371330.34841292X-RAY DIFFRACTION99
6.4394-6.82770.39641450.34461292X-RAY DIFFRACTION100
6.8277-7.33060.35671490.33691282X-RAY DIFFRACTION99
7.3306-8.02460.27841330.29221325X-RAY DIFFRACTION100
8.0246-9.08890.26191560.26021310X-RAY DIFFRACTION100
9.0889-11.11310.25591780.24261290X-RAY DIFFRACTION99
11.1131-19.98350.30471540.30471364X-RAY DIFFRACTION98

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