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- PDB-5uj9: Cryo-EM structure of bovine multidrug resistance protein 1 (MRP1) -

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Basic information

Entry
Database: PDB / ID: 5uj9
TitleCryo-EM structure of bovine multidrug resistance protein 1 (MRP1)
Descriptorbovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1
KeywordsTRANSPORT PROTEIN / ABC transporter / multidrug resistance
Specimen sourceBos taurus / mammal / Bovine / ウシ /
MethodElectron microscopy (3.49 Å resolution / Particle / Single particle)
AuthorsJohnson, Z.L. / 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 17, 2017 / Release: Feb 22, 2017
RevisionDateData content typeGroupProviderType
1.0Feb 22, 2017Structure modelrepositoryInitial release
1.1Mar 15, 2017Structure modelDatabase references
1.2Mar 22, 2017Structure modelDatabase references
1.3Mar 29, 2017Structure modelSource and taxonomy

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,7021
Polyers159,7021
Non-polymers00
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

Cellular component

Molecular function

Biological process

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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: bovine multidrug resistance protein 1 (MRP1) / Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Molecular weightValue: 0.17 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Bos taurus
Source (recombinant)Cell: HEK293S GntI- / Organism: Homo sapiens / Plasmid: Baculovirus
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameBuffer ID
1150mMKCl1
250mMTris1
32mMMgCl21
42mMDTT1
50.06%Digitonin1
63mMFos-Choline-8, fluorinated1
SpecimenConc.: 4.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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 / Nominal defocus max: 2400 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 80 kelvins
Image recordingAverage exposure time: 7 sec. / Electron dose: 84 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2232
Image scansDimension width: 3710 / Dimension height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1Relion1.4PARTICLE SELECTION1
2Serial EMIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7COOT0.8.7MODEL FITTING1
9RELION1.4INITIAL EULER ASSIGNMENT1
10FREALIGNFINAL EULER ASSIGNMENT1
12FREALIGNRECONSTRUCTION1
13PHENIX1.11MODEL REFINEMENT1
14REFMACCCP4 7.0MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 251986
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 251986 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: RECIPROCAL
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall ESU RSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1265.842-6.20-0.402.194.380.611.820.969HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.285640.285643.49148.008828299.990.4480.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 9857
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01910042
ELECTRON MICROSCOPYr_bond_other_d0.0000.0209686
ELECTRON MICROSCOPYr_angle_refined_deg1.0281.95713640
ELECTRON MICROSCOPYr_angle_other_deg3.7913.00022312
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.5485.0001286
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.40223.795390
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.13015.0001667
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.64115.00055
ELECTRON MICROSCOPYr_chiral_restr0.0540.2001619
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.02011130
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0202045
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_it6.37427.3975171
ELECTRON MICROSCOPYr_mcbond_other6.37327.3955170
ELECTRON MICROSCOPYr_mcangle_it10.48941.0736448
ELECTRON MICROSCOPYr_mcangle_other10.48841.0756449
ELECTRON MICROSCOPYr_scbond_it6.42426.8854871
ELECTRON MICROSCOPYr_scbond_other6.42326.8794869
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other11.37440.2817192
ELECTRON MICROSCOPYr_long_range_B_refined17.84012003
ELECTRON MICROSCOPYr_long_range_B_other17.84012004
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.49 Å / R factor R work: 0.765 / Lowest resolution: 3.581 Å / Number reflection R free: 0 / Number reflection R work: 6547 / Total number of bins used: 20 / Percent reflection obs: 99.91

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