[English] 日本語
Yorodumi
- EMDB-12043: AcrB in cycloalkane amphipol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12043
TitleAcrB in cycloalkane amphipol
Map data
Sample
  • Complex: AcrB
    • Protein or peptide: Efflux pump membrane transporter
Keywordsdrug exporter / membrane protein / amphipol
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHiggins AJ / Flynn AJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018561/1/ United Kingdom
CitationJournal: Commun Biol / Year: 2021
Title: Cycloalkane-modified amphiphilic polymers provide direct extraction of membrane proteins for CryoEM analysis.
Authors: Anna J Higgins / Alex J Flynn / Anaïs Marconnet / Laura J Musgrove / Vincent L G Postis / Jonathan D Lippiat / Chun-Wa Chung / Tom Ceska / Manuela Zoonens / Frank Sobott / Stephen P Muench /
Abstract: Membrane proteins are essential for cellular growth, signalling and homeostasis, making up a large proportion of therapeutic targets. However, the necessity for a solubilising agent to extract them ...Membrane proteins are essential for cellular growth, signalling and homeostasis, making up a large proportion of therapeutic targets. However, the necessity for a solubilising agent to extract them from the membrane creates challenges in their structural and functional study. Although amphipols have been very effective for single-particle electron cryo-microscopy (cryoEM) and mass spectrometry, they rely on initial detergent extraction before exchange into the amphipol environment. Therefore, circumventing this pre-requirement would be a big advantage. Here we use an alternative type of amphipol: a cycloalkane-modified amphiphile polymer (CyclAPol) to extract Escherichia coli AcrB directly from the membrane and demonstrate that the protein can be isolated in a one-step purification with the resultant cryoEM structure achieving 3.2 Å resolution. Together this work shows that cycloalkane amphipols provide a powerful approach for the study of membrane proteins, allowing native extraction and high-resolution structure determination by cryoEM.
History
DepositionDec 5, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7b5p
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12043.png

Downloads & links

-
Map

FileDownload / File: emd_12043.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0224 / Movie #1: 0.016
Minimum - Maximum-0.06397724 - 0.113237076
Average (Standard dev.)-0.00001657938 (±0.0046137865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0640.113-0.000

-
Supplemental data

-
Sample components

-
Entire : AcrB

EntireName: AcrB
Components
  • Complex: AcrB
    • Protein or peptide: Efflux pump membrane transporter

-
Supramolecule #1: AcrB

SupramoleculeName: AcrB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 113.919477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPRPNFFIDR PIFAWVIAII IMLAGGLAIL KLPVAQYPTI APPAVTISAS YPGADAKTVQ DTVTQVIEQN MNGIDNLMYM SSNSDSTGT VQITLTFESG TDADIAQVQV QNKLQLAMPL LPQEVQQQGV SVEKSSSSFL MVVGVINTDG TMTQEDISDY V AANMKDAI ...String:
MPRPNFFIDR PIFAWVIAII IMLAGGLAIL KLPVAQYPTI APPAVTISAS YPGADAKTVQ DTVTQVIEQN MNGIDNLMYM SSNSDSTGT VQITLTFESG TDADIAQVQV QNKLQLAMPL LPQEVQQQGV SVEKSSSSFL MVVGVINTDG TMTQEDISDY V AANMKDAI SRTSGVGDVQ LFGSQYAMRI WMNPNELNKF QLTPVDVITA IKAQNAQVAA GQLGGTPPVK GQQLNASIIA QT RLTSTEE FGKILLKVNQ DGSRVLLRDV AKIELGGENY DIIAEFNGQP ASGLGIKLAT GANALDTAAA IRAELAKMEP FFP SGLKIV YPYDTTPFVK ISIHEVVKTL VEAIILVFLV MYLFLQNFRA TLIPTIAVPV VLLGTFAVLA AFGFSINTLT MFGM VLAIG LLVDDAIVVV ENVERVMAEE GLPPKEATRK SMGQIQGALV GIAMVLSAVF VPMAFFGGST GAIYRQFSIT IVSAM ALSV LVALILTPAL CATMLKPIAK GDHGEGKKGF FGWFNRMFEK STHHYTDSVG GILRSTGRYL VLYLIIVVGM AYLFVR LPS SFLPDEDQGV FMTMVQLPAG ATQERTQKVL NEVTHYYLTK EKNNVESVFA VNGFGFAGRG QNTGIAFVSL KDWADRP GE ENKVEAITMR ATRAFSQIKD AMVFAFNLPA IVELGTATGF DFELIDQAGL GHEKLTQARN QLLAEAAKHP DMLTSVRP N GLEDTPQFKI DIDQEKAQAL GVSINDINTT LGAAWGGSYV NDFIDRGRVK KVYVMSEAKY RMLPDDIGDW YVRAADGQM VPFSAFSSSR WEYGSPRLER YNGLPSMEIL GQAAPGKSTG EAMELMEQLA SKLPTGVGYD WTGMSYQERL SGNQAPSLYA ISLIVVFLC LAALYESWSI PFSVMLVVPL GVIGALLAAT FRGLTNDVYF QVGLLTTIGL SAKNAILIVE FAKDLMDKEG K GLIEATLD AVRMRLRPIL MTSLAFILGV MPLVISTGAG SGAQNAVGTG VMGGMVTATV LAIFFVPVFF VVVRRRFSRK NE DIEHSHT VDHH

UniProtKB: Efflux pump membrane transporter

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6baj

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100932
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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