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- EMDB-66716: C3 map of MdtF from 200kV Talos Arctica dataset -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-66716
TitleC3 map of MdtF from 200kV Talos Arctica dataset
Map data
Sample
  • Organelle or cellular component: Cryo-EM map of MdtF from 200kV Talos Arctica dataset
KeywordsMembrane protein / E.coli. / Cryo-EM / Efflux pump. / TRANSPORT PROTEIN
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDutta S / Padmanaban S / Fernando Rencilin C
Funding support India, 3 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Science and Engineering Research Board (SERB)CRG/2022/002674 India
CitationJournal: To Be Published
Title: Structural insights and conformational dynamics of the MdtB and MdtF Efflux Pumps in Escherichia coli
Authors: Dutta S / Padmanaban S / Fernando Rencilin C
History
DepositionOct 24, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66716.png

Downloads & links

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Map

FileDownload / File: emd_66716.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0621
Minimum - Maximum-0.15302455 - 0.3874911
Average (Standard dev.)-0.00041292552 (±0.0150633585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66716_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66716_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM map of MdtF from 200kV Talos Arctica dataset

EntireName: Cryo-EM map of MdtF from 200kV Talos Arctica dataset
Components
  • Organelle or cellular component: Cryo-EM map of MdtF from 200kV Talos Arctica dataset

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Supramolecule #1: Cryo-EM map of MdtF from 200kV Talos Arctica dataset

SupramoleculeName: Cryo-EM map of MdtF from 200kV Talos Arctica dataset / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 569547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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