[English] 日本語
Yorodumi
- EMDB-20945: Cryo-EM structure of wild-type bovine multidrug resistance protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20945
TitleCryo-EM structure of wild-type bovine multidrug resistance protein 1 (MRP1) under active turnover conditions
Map data
Samplebovine multidrug resistance protein 1 (MRP1)
  • Multidrug resistance-associated protein 1
  • (ligand) x 4
Function / homology
Function and homology information


glutathione transmembrane transport / sphingolipid translocation / ABC-type glutathione-S-conjugate transporter / ABC-type transmembrane transporter activity / leukotriene transport / ATPase-coupled glutathione S-conjugate transmembrane transporter activity / glutathione transmembrane transporter activity / ATPase-coupled lipid transmembrane transporter activity / ABC-type xenobiotic transporter / export across plasma membrane ...glutathione transmembrane transport / sphingolipid translocation / ABC-type glutathione-S-conjugate transporter / ABC-type transmembrane transporter activity / leukotriene transport / ATPase-coupled glutathione S-conjugate transmembrane transporter activity / glutathione transmembrane transporter activity / ATPase-coupled lipid transmembrane transporter activity / ABC-type xenobiotic transporter / export across plasma membrane / transepithelial transport / ATPase-coupled xenobiotic transmembrane transporter activity / phospholipid translocation / xenobiotic transport / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / basal plasma membrane / positive regulation of inflammatory response / cellular response to amyloid-beta / transmembrane transport / basolateral plasma membrane / response to drug / ATPase activity / integral component of plasma membrane / membrane / ATP binding
ABC transporter-like / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / ABC transporter type 1, transmembrane domain / Multi drug resistance-associated protein / AAA+ ATPase domain
Multidrug resistance-associated protein 1
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsJohnson ZL / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2020
Title: Characterization of the kinetic cycle of an ABC transporter by single-molecule and cryo-EM analyses.
Authors: Ling Wang / Zachary Lee Johnson / Michael R Wasserman / Jesper Levring / Jue Chen / Shixin Liu /
Abstract: ATP-binding cassette (ABC) transporters are molecular pumps ubiquitous across all kingdoms of life. While their structures have been widely reported, the kinetics governing their transport cycles ...ATP-binding cassette (ABC) transporters are molecular pumps ubiquitous across all kingdoms of life. While their structures have been widely reported, the kinetics governing their transport cycles remain largely unexplored. Multidrug resistance protein 1 (MRP1) is an ABC exporter that extrudes a variety of chemotherapeutic agents and native substrates. Previously, the structures of MRP1 were determined in an inward-facing (IF) or outward-facing (OF) conformation. Here, we used single-molecule fluorescence spectroscopy to track the conformational changes of bovine MRP1 (bMRP1) in real time. We also determined the structure of bMRP1 under active turnover conditions. Our results show that substrate stimulates ATP hydrolysis by accelerating the IF-to-OF transition. The rate-limiting step of the transport cycle is the dissociation of the nucleotide-binding-domain dimer, while ATP hydrolysis per se does not reset MRP1 to the resting state. The combination of structural and kinetic data illustrates how different conformations of MRP1 are temporally linked and how substrate and ATP alter protein dynamics to achieve active transport.
Validation ReportPDB-ID: 6uy0

SummaryFull reportAbout validation report
History
DepositionNov 9, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseJun 10, 2020-
UpdateJun 10, 2020-
Current statusJun 10, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6uy0
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20945.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å
1.03 Å/pix.
x 320 pix.
= 329.6 Å
1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.09093327 - 0.1840185
Average (Standard dev.)0.000000103 (±0.0038368243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ180180180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0910.1840.000

-
Supplemental data

-
Sample components

+
Entire bovine multidrug resistance protein 1 (MRP1)

EntireName: bovine multidrug resistance protein 1 (MRP1) / Number of components: 6

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

ProteinName: bovine multidrug resistance protein 1 (MRP1) / 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-

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

ProteinName: Multidrug resistance-associated protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 172.862562 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human)

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

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

+
Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

+
Component #5: ligand, MAGNESIUM ION

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

+
Component #6: ligand, CHOLESTEROL

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

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 5.3 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

-
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: 75 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (80.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 3993

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81078
3D reconstructionSoftware: RELION / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: RECIPROCAL
Input PDB model: 6BHU
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more