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- EMDB-8560: Cryo-EM structure of bovine multidrug resistance protein 1 (MRP1)... -

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Basic information

Entry
Database: EMDB / ID: 8560
TitleCryo-EM structure of bovine multidrug resistance protein 1 (MRP1) bound to leukotriene C4
Samplebovine multidrug resistance protein 1 (MRP1) complexed with leukotriene C4
SourceBos taurus / mammal / ウシ /
Map dataFull map translated into unit cell used for reciprocal space refinement, sharpened with a B-factor of -100 A^2 and a resolution cutoff of 3.34 A
Methodsingle particle reconstruction, at 3.34 Å resolution
AuthorsJohnson ZL / 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 ReportPDB-ID: 5uja

SummaryFull reportAbout validation report
DateDeposition: Jan 17, 2017 / Header (metadata) release: Feb 22, 2017 / Map release: Feb 22, 2017 / Last update: May 24, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5uja
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_8560.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

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AxesY (Sec.)X (Row.)Z (Col.)
384 pix
0.26 Å/pix.
= 98.999 Å
384 pix
0.38 Å/pix.
= 146.001 Å
384 pix
0.28 Å/pix.
= 107.002 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.38021 Å / Y: 0.25781 Å / Z: 0.27865 Å
Density
Contour Level:1.6 (by author), 1.6 (movie #1):
Minimum - Maximum-4.154357 - 5.2137184
Average (Standard dev.)0.21231677 (0.61837626)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA: 146.00064 Å / B: 98.99904 Å / C: 107.001595 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.38021093750.257809895833330.27865104166667
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z146.00198.999107.002
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-4.1545.2140.212

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Supplemental data

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Sample components

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Entire bovine multidrug resistance protein 1 (MRP1) complexed with leuko...

EntireName: bovine multidrug resistance protein 1 (MRP1) complexed with leukotriene C4
Number of components: 3
MassTheoretical: 170 kDa

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Component #1: protein, bovine multidrug resistance protein 1 (MRP1) complexed w...

ProteinName: bovine multidrug resistance protein 1 (MRP1) complexed with leukotriene C4
Recombinant expression: No
MassTheoretical: 170 kDa
SourceSpecies: Bos taurus / mammal / ウシ /
Source (engineered)Expression System: Homo sapiens / human / Vector: Baculovirus / Cell of expression system: HEK293S GntI-

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Component #2: protein, bovine multidrug resistance protein 1 (MRP1),Multidrug r...

ProteinName: bovine multidrug resistance protein 1 (MRP1),Multidrug resistance-associated protein 1
Recombinant expression: No
MassTheoretical: 159.701922 kDa
Source (engineered)Expression System: Bos taurus / mammal / ウシ /

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Component #3: ligand, (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4...

LigandName: (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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.625774 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 4.65 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 84 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 2400 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80 - 100 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2302

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 203732
3D reconstructionSoftware: FREALIGN / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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