[English] 日本語
Yorodumi
- EMDB-6021: Conformational Spectrum of Multidrug ABC Transporters Revealed by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6021
TitleConformational Spectrum of Multidrug ABC Transporters Revealed by Single Particle Electron Microscopy
Map dataP-gp in inward-facing conformation
Sample
  • Sample: Pgp_m stabilised in lipid/amphiphilic environment - inward-facing 6.0 nm opening
  • Protein or peptide: P-glycoprotein
KeywordsABC transporter / P-gp / MsbA
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsMoeller A / Chang Lee S / Tao H / Speir S / Chang G / Urbatsch IL / Potter CS / Carragher B / Zhang Q
CitationJournal: Structure / Year: 2015
Title: Distinct conformational spectrum of homologous multidrug ABC transporters.
Authors: Arne Moeller / Sung Chang Lee / Houchao Tao / Jeffrey A Speir / Geoffrey Chang / Ina L Urbatsch / Clinton S Potter / Bridget Carragher / Qinghai Zhang /
Abstract: ATP-binding cassette (ABC) exporters are ubiquitously found in all kingdoms of life and their members play significant roles in mediating drug pharmacokinetics and multidrug resistance in the clinic. ...ATP-binding cassette (ABC) exporters are ubiquitously found in all kingdoms of life and their members play significant roles in mediating drug pharmacokinetics and multidrug resistance in the clinic. Significant questions and controversies remain regarding the relevance of their conformations observed in X-ray structures, their structural dynamics, and mechanism of transport. Here, we used single particle electron microscopy (EM) to delineate the entire conformational spectrum of two homologous ABC exporters (bacterial MsbA and mammalian P-glycoprotein) and the influence of nucleotide and substrate binding. Newly developed amphiphiles in complex with lipids that support high protein stability and activity enabled EM visualization of individual complexes in a membrane-mimicking environment. The data provide a comprehensive view of the conformational flexibility of these ABC exporters under various states and demonstrate not only similarities but striking differences between their mechanistic and energetic regulation of conformational changes.
History
DepositionAug 7, 2014-
Header (metadata) releaseSep 24, 2014-
Map releaseFeb 4, 2015-
UpdateSep 16, 2015-
Current statusSep 16, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6021.tif

Downloads & links

-
Map

FileDownload / File: emd_6021.map.gz / Format: CCP4 / Size: 245.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationP-gp in inward-facing conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.46 Å/pix.
x 40 pix.
= 218.2 Å		5.46 Å/pix.
x 40 pix.
= 218.2 Å		5.46 Å/pix.
x 40 pix.
= 218.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.455 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.88400793 - 2.35042024
Average (Standard dev.)-0.01407188 (±0.2861397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-20
Dimensions404040
Spacing404040
CellA=B=C: 218.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.4555.4555.455
M x/y/z404040
origin x/y/z0.0000.0000.000
length x/y/z218.200218.200218.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS-20-20-20
NC/NR/NS404040
D min/max/mean-0.8842.350-0.014

-
Supplemental data

-
Sample components

-
Entire : Pgp_m stabilised in lipid/amphiphilic environment - inward-facing...

EntireName: Pgp_m stabilised in lipid/amphiphilic environment - inward-facing 6.0 nm opening
Components
  • Sample: Pgp_m stabilised in lipid/amphiphilic environment - inward-facing 6.0 nm opening
  • Protein or peptide: P-glycoprotein

-
Supramolecule #1000: Pgp_m stabilised in lipid/amphiphilic environment - inward-facing...

SupramoleculeName: Pgp_m stabilised in lipid/amphiphilic environment - inward-facing 6.0 nm opening
type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 140 KDa

-
Macromolecule #1: P-glycoprotein

MacromoleculeName: P-glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: P-gp, Pgp, MDR1A / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: mouse / Location in cell: plasma membrane
Molecular weightTheoretical: 140 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus) / Recombinant strain: Gs115 / Recombinant plasmid: pHIL-mdr3.5-His6

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

StainingType: NEGATIVE / Details: uranyl formate
GridDetails: thin carbon over holes
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F20
DateAug 12, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 456 / Average electron dose: 45 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsRCT reconstruction
CTF correctionDetails: whole micrograph - unitilted images
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: Appion, Spider, Sparx, Eman2 / Number images used: 229

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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