[English] 日本語
Yorodumi
- EMDB-5526: Electron cryo-microscopy of ABC BmrA in 13-fold symmetry rings -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5526
TitleElectron cryo-microscopy of ABC BmrA in 13-fold symmetry rings
Map dataReconstruction of BmrA into lipid bilayer. D13 symmetrized reconstruction. 39 homodimers are inserted.
Sample
  • Sample: BmrA reconstituted at high density into lipid bilayer.
  • Protein or peptide: BmrA
KeywordsABC transporter / exporter / bmra / yvcc / transmembrane protein / reconstitution into lipids / membrane protein
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsFribourg PF / Chami M / Sorzano CO / Gubellini F / Marabini R / Marco S / Jault JM / Levy D
CitationJournal: J Mol Biol / Year: 2014
Title: 3D cryo-electron reconstruction of BmrA, a bacterial multidrug ABC transporter in an inward-facing conformation and in a lipidic environment.
Authors: Pierre Frederic Fribourg / Mohamed Chami / Carlos Oscar S Sorzano / Francesca Gubellini / Roberto Marabini / Sergio Marco / Jean-Michel Jault / Daniel Lévy /
Abstract: ABC (ATP-binding cassette) membrane exporters are efflux transporters of a wide diversity of molecule across the membrane at the expense of ATP. A key issue regarding their catalytic cycle is whether ...ABC (ATP-binding cassette) membrane exporters are efflux transporters of a wide diversity of molecule across the membrane at the expense of ATP. A key issue regarding their catalytic cycle is whether or not their nucleotide-binding domains (NBDs) are physically disengaged in the resting state. To settle this controversy, we obtained structural data on BmrA, a bacterial multidrug homodimeric ABC transporter, in a membrane-embedded state. BmrA in the apostate was reconstituted in lipid bilayers forming a mixture of ring-shaped structures of 24 or 39 homodimers. Three-dimensional models of the ring-shaped structures of 24 or 39 homodimers were calculated at 2.3 nm and 2.5 nm resolution from cryo-electron microscopy, respectively. In these structures, BmrA adopts an inward-facing open conformation similar to that found in mouse P-glycoprotein structure with the NBDs separated by 3 nm. Both lipidic leaflets delimiting the transmembrane domains of BmrA were clearly resolved. In planar membrane sheets, the NBDs were even more separated. BmrA in an ATP-bound conformation was determined from two-dimensional crystals grown in the presence of ATP and vanadate. A projection map calculated at 1.6 nm resolution shows an open outward-facing conformation. Overall, the data are consistent with a mechanism of drug transport involving large conformational changes of BmrA and show that a bacterial ABC exporter can adopt at least two open inward conformations in lipid membrane.
History
DepositionNov 2, 2012-
Header (metadata) releaseNov 21, 2012-
Map releaseNov 21, 2012-
UpdateMay 14, 2014-
Current statusMay 14, 2014Processing site: RCSB / 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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5526.tif

Downloads & links

-
Map

FileDownload / File: emd_5526.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of BmrA into lipid bilayer. D13 symmetrized reconstruction. 39 homodimers are inserted.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 200 pix.
= 500. Å		2.5 Å/pix.
x 200 pix.
= 500. Å		2.5 Å/pix.
x 200 pix.
= 500. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.03009361 - 0.04987804
Average (Standard dev.)0.00066482 (±0.01053878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 500.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z500.000500.000500.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0300.0500.001

-
Supplemental data

-
Sample components

-
Entire : BmrA reconstituted at high density into lipid bilayer.

EntireName: BmrA reconstituted at high density into lipid bilayer.
Components
  • Sample: BmrA reconstituted at high density into lipid bilayer.
  • Protein or peptide: BmrA

-
Supramolecule #1000: BmrA reconstituted at high density into lipid bilayer.

SupramoleculeName: BmrA reconstituted at high density into lipid bilayer.
type: sample / ID: 1000
Oligomeric state: 39 Homodimers of BmrA inserted into lipid bilayer
Number unique components: 1
Molecular weightExperimental: 5.07 MDa / Theoretical: 5.07 MDa

-
Macromolecule #1: BmrA

MacromoleculeName: BmrA / type: protein_or_peptide / ID: 1 / Name.synonym: YvcC / Details: 39 homodimers of inserted into lipid bilayer / Number of copies: 39 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightExperimental: 5.07 MDa / Theoretical: 5.07 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8 / Details: 50mM HEPES, 100mM NaCl
GridDetails: Ted Pella inc. holey formvar grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: specimen linked to a Ni++-NTA-DOGS/DOPC lipid monolayer
Method: Blot for 3 seconds before plunging.

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateJan 1, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Number real images: 102 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsXmipp CL2D classification and Projection matching refinement with Invert Fourier 3D reconstruction
CTF correctionDetails: Micrograph based
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 1229

-
Atomic model buiding 1

Initial modelPDB ID:

3g61

SoftwareName: Chimera
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation factor

+
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