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- PDB-5uja: Cryo-EM structure of bovine multidrug resistance protein 1 (MRP1)... -

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Basic information

Entry
Database: PDB / ID: 5uja
TitleCryo-EM structure of bovine multidrug resistance protein 1 (MRP1) bound to leukotriene C4
Descriptorbovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1
KeywordsPROTEIN TRANSPORT / ABC transporter / multidrug resistance / leukotriene C4 / LTC4
Specimen sourceBos taurus / mammal / Bovine / ウシ /
MethodElectron microscopy (3.34 A resolution / Single particle)
AuthorsJohnson, Z.E. / Chen, J.
CitationCell, 2017, 168, 1075-1085.e9

Cell, 2017, 168, 1075-1085.e9 StrPapers
Structural Basis of Substrate Recognition by the Multidrug Resistance Protein MRP1.
Zachary Lee Johnson / Jue Chen

DateDeposition: Jan 17, 2017 / Release: Feb 22, 2017 / Last modification: Mar 22, 2017

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Assembly

Deposited unit
A: bovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,3282
Polyers159,7021
Non-polymers6261
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)bovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1 / ATP-binding cassette sub-family C member 1 / Leukotriene C(4) transporter / LTC4 transporter


Mass: 159701.922 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus / mammal / ウシ / / References: UniProt: Q8HXQ5
#2: ChemicalChemComp-LTX / (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-(2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid


Mass: 625.774 Da / Num. of mol.: 1 / Formula: C30H47N3O9S
Sequence detailsResidues 31-194, corresponding to TMD0, are modeled as poly-alanine. The register in this region could not be confidently established and thus the numbering assigned to the residues is putative. The poly-alanine regions have been renamed as unknown

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: bovine multidrug resistance protein 1 (MRP1) complexed with leukotriene C4
Type: COMPLEX
Specimen supportGrid material: GOLD
Grid type: Quantifoil R1.2/1.3 400-mesh Au Holey Carbon Grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 37000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
ComputingStructure refinement: REFMAC 5.8.0158
3D reconstructionResolution: 3.34 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 203732
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: RECIPROCAL
Refine

B iso mean: 285.432 A2 / Aniso B11: -5.33 A2 / Aniso B12: 0.13 A2 / Aniso B13: 0.55 A2 / Aniso B22: 4.83 A2 / Aniso B23: 2.48 A2 / Aniso B33: 0.5 A2 / Correlation coeff Fo to Fc: 0.973 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / R factor R work: 0.27676 / R factor obs: 0.27676 / Highest resolution: 3.34 A / Lowest resolution: 146 A / Number reflection obs: 86964 / Percent reflection obs: 99.99 / Overall ESU R: 0.423 / Solvent ion probe radii: 0.8 A / Solvent shrinkage radii: 0.8 A / Solvent vdw probe radii: 1.2 A / Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES / Solvent model details: MASK

Refine id
1
ELECTRON MICROSCOPY
Number of atoms included #1Total: 9900
Refine LS restraints
Refine idTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01910084
ELECTRON MICROSCOPYr_bond_other_d0.0000.0209729
ELECTRON MICROSCOPYr_angle_refined_deg1.0511.96113690
ELECTRON MICROSCOPYr_angle_other_deg3.7983.00022413
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.4395.0001286
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.42523.795390
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.12215.0001667
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.00515.00055
ELECTRON MICROSCOPYr_chiral_restr0.0560.2001623
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02011168
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0202055
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.23129.3935171
ELECTRON MICROSCOPYr_mcbond_other7.22829.3915170
ELECTRON MICROSCOPYr_mcangle_it11.70044.0676448
ELECTRON MICROSCOPYr_mcangle_other11.69944.0696449
ELECTRON MICROSCOPYr_scbond_it6.95928.8934913
ELECTRON MICROSCOPYr_scbond_other6.95728.8934912
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.35943.2987243
ELECTRON MICROSCOPYr_long_range_B_refined19.49012268
ELECTRON MICROSCOPYr_long_range_B_other19.48912269
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.34 A / R factor R work: 0.601 / Lowest resolution: 3.427 A / Number reflection R free: 0 / Number reflection R work: 6479 / Total number of bins used: 20 / Percent reflection obs: 99.91

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