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- EMDB-7099: Cryo-EM structure of ATP-bound, outward-facing bovine multidrug r... -

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Basic information

Entry
Database: EMDB / ID: 7099
TitleCryo-EM structure of ATP-bound, outward-facing bovine multidrug resistance protein 1 (MRP1)
Map dataFull map scaled to model, B-factor sharpened with a sharpening factor of -75 A^2.
Samplebovine multidrug resistance protein 1 (MRP1) E1454Q
  • Multidrug resistance-associated protein 1
  • (ligand) x 3
Function / homologyMulti drug resistance-associated protein / ABC transporter integral membrane type-1 fused domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / ABC transporter / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain / AAA+ ATPase domain ...Multi drug resistance-associated protein / ABC transporter integral membrane type-1 fused domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / ABC transporter / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain / AAA+ ATPase domain / ABC transporter-like / ATP-binding cassette, ABC transporter-type domain profile. / glutathione transmembrane transport / glutathione transmembrane transporter activity / glutathione S-conjugate-exporting ATPase activity / xenobiotic transport / xenobiotic transmembrane transporting ATPase activity / drug transmembrane transport / basolateral plasma membrane / integral component of plasma membrane / ATP binding / Multidrug resistance-associated protein 1
Function and homology information
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 3.14 Å resolution
AuthorsJohnson ZL / Chen J
CitationJournal: Cell / Year: 2018
Title: ATP Binding Enables Substrate Release from Multidrug Resistance Protein 1.
Authors: Zachary Lee Johnson / Jue Chen
Abstract: The multidrug resistance protein MRP1 is an ATP-driven pump that confers resistance to chemotherapy. Previously, we have shown that intracellular substrates are recruited to a bipartite binding site ...The multidrug resistance protein MRP1 is an ATP-driven pump that confers resistance to chemotherapy. Previously, we have shown that intracellular substrates are recruited to a bipartite binding site when the transporter rests in an inward-facing conformation. A key question remains: how are high-affinity substrates transferred across the membrane and released outside the cell? Using electron cryomicroscopy, we show here that ATP binding opens the transport pathway to the extracellular space and reconfigures the substrate-binding site such that it relinquishes its affinity for substrate. Thus, substrate is released prior to ATP hydrolysis. With this result, we now have a complete description of the conformational cycle that enables substrate transfer in a eukaryotic ABC exporter.
Validation ReportPDB-ID: 6bhu

SummaryFull reportAbout validation report
DateDeposition: Oct 31, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Dec 27, 2017 / Last update: Oct 3, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6bhu
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7099.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
0.82 Å/pix.
= 313.728 Å
384 pix
0.82 Å/pix.
= 313.728 Å
384 pix
0.82 Å/pix.
= 313.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.817 Å
Density
Contour Level:1.5 (by author), 1.5 (movie #1):
Minimum - Maximum-4.9317555 - 9.895077000000001
Average (Standard dev.)0.008479072 (0.23633268)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 313.728 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8170.8170.817
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z313.728313.728313.728
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-4.9329.8950.008

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Supplemental data

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Sample components

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Entire bovine multidrug resistance protein 1 (MRP1) E1454Q

EntireName: bovine multidrug resistance protein 1 (MRP1) E1454Q / Number of components: 5

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Component #1: protein, bovine multidrug resistance protein 1 (MRP1) E1454Q

ProteinName: bovine multidrug resistance protein 1 (MRP1) E1454Q / Recombinant expression: No
MassTheoretical: 170 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human) / Vector: Baculovirus / Cell of expression system: HEK293S GntI-

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Component #2: protein, Multidrug resistance-associated protein 1

ProteinName: Multidrug resistance-associated protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 183.074062 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #5: ligand, CHOLESTEROL

LigandName: CHOLESTEROL / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.386654 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4.9 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: 37000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4210

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 354752
3D reconstructionSoftware: FREALIGN / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: RECIPROCAL
Output model

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