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- PDB-4q9l: P-glycoprotein cocrystallised with QZ-Phe -

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Basic information

Entry
Database: PDB / ID: 4q9l
TitleP-glycoprotein cocrystallised with QZ-Phe
Components
  • (30F)F(30F)F(30F)F Peptide
  • Multidrug resistance protein 1AMultiple drug resistance
KeywordsHYDROLASE/HYDROLASE INHIBITOR / membrane protein / transporter / HYDROLASE-HYDROLASE INHIBITOR complex
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
cyclic-tris-phenylselenazole / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsMcGrath, A.P. / Szewczyk, P. / Chang, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Snapshots of ligand entry, malleable binding and induced helical movement in P-glycoprotein.
Authors: Szewczyk, P. / Tao, H. / McGrath, A.P. / Villaluz, M. / Rees, S.D. / Lee, S.C. / Doshi, R. / Urbatsch, I.L. / Zhang, Q. / Chang, G.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2May 25, 2016Group: Structure summary
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details

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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: (30F)F(30F)F(30F)F Peptide
C: (30F)F(30F)F(30F)F Peptide


Theoretical massNumber of molelcules
Total (without water)143,7273
Polymers143,7273
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.340, 138.420, 184.960
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: 141919.953 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 / Plasmid: pPICZ / Production host: Pichia Pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P21447, xenobiotic-transporting ATPase
#2: Protein/peptide (30F)F(30F)F(30F)F Peptide


Type: Peptide-like / Class: Inhibitor / Mass: 903.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: cyclic-tris-phenylselenazole
Nonpolymer detailsTHE PLACEMENT OF THE BOUND CYCLIC-TRIS-PHENYLSELENAZOLE PEPTIDE-LIKE LIGAND WAS CONFIRMED USING THE ...THE PLACEMENT OF THE BOUND CYCLIC-TRIS-PHENYLSELENAZOLE PEPTIDE-LIKE LIGAND WAS CONFIRMED USING THE ANOMALOUS SCATTERING FROM THE INCORPORATED SELENIUMS, SEE PRIMARY CITATION FOR DETAILS

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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: 68.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7
Details: PEG 600, Li2O4S, HEPES, EDTA, pH 7, vapor diffusion, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97958 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 3.8→86.34 Å / Num. all: 22385 / Num. obs: 22385 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 181.31 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.066 / Rsym value: 0.058 / Net I/av σ(I): 6.712 / Net I/σ(I): 10.9 / Num. measured all: 97970
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.8-4.014.40.6961.11418132210.3660.6962.2100
4.01-4.254.40.4181.81359830740.220.4183.599.9
4.25-4.544.40.2233.41283328970.1180.223699.9
4.54-4.914.40.1425.31182126730.0750.1428.699.9
4.91-5.374.40.1066.91101025000.0560.10610.5100
5.37-6.014.40.0897.6996522720.0470.08911.7100
6.01-6.944.40.06610.2876320060.0350.06615.799.9
6.94-8.54.30.05111.1747617260.0270.0512399.7
8.5-12.024.20.03317.8570513460.0180.03330.699.5
12.02-86.343.90.03617.226186700.020.03630.684.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→76.897 Å / SU ML: 0.62 / σ(F): 1.04 / Phase error: 35.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2931 2130 5.1 %
Rwork0.2585 --
obs0.2603 -99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 172.2986 Å2
Refinement stepCycle: LAST / Resolution: 3.8→76.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9303 0 0 0 9303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049484
X-RAY DIFFRACTIONf_angle_d0.75512821
X-RAY DIFFRACTIONf_dihedral_angle_d12.3713426
X-RAY DIFFRACTIONf_chiral_restr0.0291465
X-RAY DIFFRACTIONf_plane_restr0.0031627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.88840.4351360.38822662X-RAY DIFFRACTION100
3.8884-3.98570.41621500.34212662X-RAY DIFFRACTION100
3.9857-4.09340.36111460.32512669X-RAY DIFFRACTION99
4.0934-4.21390.32421350.31562632X-RAY DIFFRACTION100
4.2139-4.34990.33881490.28532675X-RAY DIFFRACTION100
4.3499-4.50530.29521010.26932716X-RAY DIFFRACTION100
4.5053-4.68570.36141110.25562644X-RAY DIFFRACTION99
4.6857-4.89890.32591300.26522676X-RAY DIFFRACTION100
4.8989-5.15710.30411500.25492664X-RAY DIFFRACTION100
5.1571-5.48020.2711550.24562644X-RAY DIFFRACTION100
5.4802-5.90320.35251570.27222647X-RAY DIFFRACTION100
5.9032-6.49690.36691390.28842672X-RAY DIFFRACTION100
6.4969-7.43640.29061850.27082629X-RAY DIFFRACTION100
7.4364-9.36650.25261510.21782638X-RAY DIFFRACTION100
9.3665-76.91240.24811350.23892441X-RAY DIFFRACTION92
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)
10.80010.15050.3481.93880.1103-0.09960.10430.8051-0.1604-0.31550.4809-0.95470.18290.2996-0.58751.4078-0.11080.44371.686-0.49011.37361.99940.29527.2914
22.19990.5193-0.70770.5339-0.04381.11990.36620.32890.62970.09730.12320.2824-0.5501-0.3725-0.5681.59180.14920.53460.78790.00161.21833.311213.86334.6811
3-0.2202-0.1860.1574-0.3683-0.0847-0.0418-0.10620.1397-0.04770.2840.4769-0.0456-0.34280.2809-0.51891.7263-0.08010.68631.6159-0.18781.651964.282816.97067.3932
47.1864-2.0687-0.90576.1524-0.45924.5093-0.0812-1.0014-0.59040.5540.32440.14950.51780.2741-0.21390.8210.01820.05060.811-0.09370.748870.158242.852656.0575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 318 )
2X-RAY DIFFRACTION2chain 'A' and (resid 319 through 740 )
3X-RAY DIFFRACTION3chain 'A' and (resid 741 through 1029 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1030 through 1278 )

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