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- PDB-4m1m: Corrected Structure of Mouse P-glycoprotein -

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Basic information

Entry
Database: PDB / ID: 4m1m
TitleCorrected Structure of Mouse P-glycoprotein
ComponentsMultidrug resistance protein 1AMultiple drug resistance
KeywordsHYDROLASE / ATP-Binding Cassette Transporter / Multidrug Efflux / Adenosine triphosphate / mercurated cysteines / Plasma membrane
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 / response to antineoplastic agent / Prednisone ADME / positive regulation of establishment of Sertoli cell barrier / ceramide translocation / terpenoid transport / ceramide floppase activity / response to glycoside / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / regulation of response to osmotic stress / cellular response to L-glutamate / ABC-family proteins mediated transport / establishment of blood-brain barrier / response to thyroxine / phosphatidylcholine floppase activity / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / xenobiotic detoxification by transmembrane export across the plasma membrane / export across plasma membrane / response to vitamin D / ABC-type xenobiotic transporter / intercellular canaliculus / transepithelial transport / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / response to vitamin A / response to glucagon / intestinal absorption / phospholipid translocation / cellular response to antibiotic / maintenance of blood-brain barrier / cellular hyperosmotic salinity response / cellular response to alkaloid / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / placenta development / regulation of chloride transport / stem cell proliferation / cellular response to estradiol stimulus / brush border membrane / circadian rhythm / G2/M transition of mitotic cell cycle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / 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 / 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 / SAD / Resolution: 3.8 Å
AuthorsLi, J. / Jaimes, K.F. / Aller, S.G.
CitationJournal: Protein Sci. / Year: 2014
Title: Refined structures of mouse P-glycoprotein.
Authors: Li, J. / Jaimes, K.F. / Aller, S.G.
History
DepositionAug 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)285,89915
Polymers283,2912
Non-polymers2,60813
Water0
1
A: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0508
Polymers141,6461
Non-polymers1,4047
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8497
Polymers141,6461
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.544, 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 / Multiple drug resistance / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 3 / P-glycoprotein 3


Mass: 141645.625 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 (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 13 / 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: 67.31 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00695 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00695 Å / Relative weight: 1
ReflectionResolution: 3.8→42.4 Å / Num. obs: 42711

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 3.8→24.888 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 4230 10.22 %
Rwork0.2117 --
obs0.2174 41385 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→24.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18365 0 13 0 18378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518703
X-RAY DIFFRACTIONf_angle_d0.9725285
X-RAY DIFFRACTIONf_dihedral_angle_d10.4516800
X-RAY DIFFRACTIONf_chiral_restr0.0652915
X-RAY DIFFRACTIONf_plane_restr0.0043213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.84310.33761250.26411080X-RAY DIFFRACTION85
3.8431-3.88810.39231460.32261195X-RAY DIFFRACTION94
3.8881-3.93530.41141230.30741022X-RAY DIFFRACTION82
3.9353-3.9850.30211100.25771040X-RAY DIFFRACTION79
3.985-4.03720.32581320.23931148X-RAY DIFFRACTION93
4.0372-4.09220.27861250.21781253X-RAY DIFFRACTION96
4.0922-4.15040.29461320.21331204X-RAY DIFFRACTION95
4.1504-4.21210.24881490.19831231X-RAY DIFFRACTION96
4.2121-4.27760.30381150.20561243X-RAY DIFFRACTION96
4.2776-4.34740.25661380.20291219X-RAY DIFFRACTION97
4.3474-4.42190.27091430.18911228X-RAY DIFFRACTION97
4.4219-4.50190.25391390.1921265X-RAY DIFFRACTION98
4.5019-4.58790.27261480.17941242X-RAY DIFFRACTION97
4.5879-4.6810.21161360.18031230X-RAY DIFFRACTION96
4.681-4.78210.22821430.17891231X-RAY DIFFRACTION97
4.7821-4.89250.24081400.18391284X-RAY DIFFRACTION98
4.8925-5.01390.25321410.1751236X-RAY DIFFRACTION98
5.0139-5.14830.23511490.18011235X-RAY DIFFRACTION97
5.1483-5.29840.271430.19341253X-RAY DIFFRACTION98
5.2984-5.46770.25581520.20481275X-RAY DIFFRACTION98
5.4677-5.66090.28751550.21111270X-RAY DIFFRACTION99
5.6609-5.88470.31431540.22661250X-RAY DIFFRACTION99
5.8847-6.14860.28471420.22891310X-RAY DIFFRACTION99
6.1486-6.46740.29761340.2151304X-RAY DIFFRACTION99
6.4674-6.86460.28951380.20481314X-RAY DIFFRACTION100
6.8646-7.38180.28081510.20591290X-RAY DIFFRACTION100
7.3818-8.10130.25351410.18471331X-RAY DIFFRACTION100
8.1013-9.2210.2221530.16731306X-RAY DIFFRACTION99
9.221-11.42720.19061800.17531316X-RAY DIFFRACTION99
11.4272-24.88850.32391530.30391350X-RAY DIFFRACTION95
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)
10.44350.98610.29021.28620.62181.36840.15910.1093-0.274-0.29450.1798-0.1718-0.0527-0.0911-0.26371.1533-0.0366-0.00130.9154-0.16630.852626.818465.06167.6698
20.83470.1542-0.04040.38890.26021.44180.0888-0.0635-0.0516-0.11430.0353-0.0844-0.22010.3726-0.13251.1538-0.05760.06930.9534-0.30880.946744.795887.344543.0982
32.80241.22540.3580.7462-0.31913.81890.8626-1.07081.05990.6922-1.00381.0457-0.6656-0.10120.32981.30480.18710.33771.0254-0.51871.496933.969197.379254.1996
40.0418-0.0339-0.3690.9710.81351.8884-0.02240.0448-0.14760.11280.02440.00380.05030.0082-0.18691.0383-0.2710.05790.9538-0.21891.295515.910759.954414.5961
51.05011.2879-0.43751.5383-0.43162.82240.2551-0.43330.06960.0321-0.4090.1562-0.11710.08460.03041.5638-0.25020.47051.3082-0.38641.3597-0.939298.501552.8468
61.4635-1.022-0.00630.3982-0.06-0.7504-0.3862-0.2005-0.43190.24620.27960.50820.30830.0262-0.00461.2317-0.01280.4631.5921-0.06421.330332.60643.922185.0585
75.3409-0.01450.62971.90260.6162.7456-0.208-0.4907-0.3755-0.21990.1105-0.2272-0.07420.13190.03550.9902-0.1090.26791.1591-0.02561.037771.53163.29247.0878
80.2057-0.153-0.69150.7365-1.4390.7710.8192-0.0448-0.47640.3087-0.659-0.1034-0.27050.13610.03790.94360.03560.37431.6019-0.48871.317851.422735.173465.7787
9-0.04610.71910.2533-1.2386-0.61890.83480.10240.31060.17820.24760.28150.36380.0978-0.3147-0.20041.327-0.04630.67181.4256-0.09842.023429.339236.596973.4087
102.7438-0.88330.61383.726-0.36530.4179-0.57150.2682-0.0937-0.37630.4796-0.89990.03860.41760.16191.448-0.12550.4191.7157-0.35871.227175.475216.048848.4603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 30 : 323 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 324 : 543 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 544 : 703 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 704 :1008 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1009 :1271 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 31 : 366 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 367 : 592 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 593 : 740 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 741 :1008 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1009 :1271 )

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