[English] 日本語
Yorodumi
- EMDB-8636: multi-drug efflux; membrane transport; RND superfamily; Drug resi... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8636
Titlemulti-drug efflux; membrane transport; RND superfamily; Drug resistance
SampleAcrABTolC in apo state
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataMutant cryoEM density map.
Methodsingle particle reconstruction, at 6.5 Å resolution
Authorswang Z / fan G
CitationElife, 2017, 6

Elife, 2017, 6 StrPapers
An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du

Validation ReportPDB-ID: 5v5s

SummaryFull reportAbout validation report
DateDeposition: Mar 15, 2017 / Header (metadata) release: Apr 19, 2017 / Map release: Apr 19, 2017 / Last update: Aug 2, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0266
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0266
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5v5s
  • Surface level: 0.0266
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_8636.map.gz (map file in CCP4 format, 219489 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
380 pix
1.06 Å/pix.
= 402.8 Å
380 pix
1.06 Å/pix.
= 402.8 Å
380 pix
1.06 Å/pix.
= 402.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.0266 (by author), 0.0266 (movie #1):
Minimum - Maximum-0.030838259 - 0.09197038
Average (Standard dev.)0.00056815404 (0.0040272484)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions380380380
Origin000
Limit379379379
Spacing380380380
CellA=B=C: 402.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z402.800402.800402.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0310.0920.001

-
Supplemental data

-
Sample components

-
Entire AcrABTolC in apo state

EntireName: AcrABTolC in apo state / Number of components: 4

-
Component #1: protein, AcrABTolC in apo state

ProteinName: AcrABTolC in apo state / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #2: protein, Outer membrane protein TolC

ProteinName: Outer membrane protein TolC / Recombinant expression: No
MassTheoretical: 48.673801 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #3: protein, Multidrug efflux pump subunit AcrA

ProteinName: Multidrug efflux pump subunit AcrA / Recombinant expression: No
MassTheoretical: 42.253551 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #4: protein, Multidrug efflux pump subunit AcrB

ProteinName: Multidrug efflux pump subunit AcrB / Recombinant expression: No
MassTheoretical: 113.681242 kDa
Source (engineered)Expression System: Escherichia coli / bacteria /

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 20 K / Humidity: 100 %
Details: a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)

-
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: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 13544
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more