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- EMDB-65063: cryo-EM structure of a chimeric EfpA dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-65063
Titlecryo-EM structure of a chimeric EfpA dimer
Map data
Sample
  • Complex: MsEfpA-XTM9
    • Protein or peptide: Putative MFS-type transporter EfpA
KeywordsPROTEIN / PROTEIN BINDING
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / transmembrane transporter activity / MFS transporter superfamily / plasma membrane / Putative MFS-type transporter EfpA
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsLi D / Sun J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: cryo-EM structure of a chimeric EfpA dimer
Authors: Li D / Sun J
History
DepositionJun 16, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65063.png

Downloads & links

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Map

FileDownload / File: emd_65063.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.)
0.89 Å/pix.
x 300 pix.
= 267. Å		0.89 Å/pix.
x 300 pix.
= 267. Å		0.89 Å/pix.
x 300 pix.
= 267. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.0017248648 - 1.7159642
Average (Standard dev.)0.0009242992 (±0.022174513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 267.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65063_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_65063_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 : MsEfpA-XTM9

EntireName: MsEfpA-XTM9
Components
  • Complex: MsEfpA-XTM9
    • Protein or peptide: Putative MFS-type transporter EfpA

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Supramolecule #1: MsEfpA-XTM9

SupramoleculeName: MsEfpA-XTM9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: Putative MFS-type transporter EfpA

MacromoleculeName: Putative MFS-type transporter EfpA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 53.460461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTALNDAERA AARVGLAARL PSWFPSWGFL SAVIAIGGMQ LLATMDSTVA IVALPKIQDE LSLSDAGRSW VITAYVLTFG GLMLLGGRL GDTIGRKRTF IVGVMLFTIA SVLCGIAWNE TTLVTARLLQ GVGAAIASPT GLALVATTFP KGPARNAATA V FGAMTAIG ...String:
MTALNDAERA AARVGLAARL PSWFPSWGFL SAVIAIGGMQ LLATMDSTVA IVALPKIQDE LSLSDAGRSW VITAYVLTFG GLMLLGGRL GDTIGRKRTF IVGVMLFTIA SVLCGIAWNE TTLVTARLLQ GVGAAIASPT GLALVATTFP KGPARNAATA V FGAMTAIG SVMGLVVGGA LTEVSWRWAF LVNVPIGLVM VYLARTALQE TNRERMKLDA AGALLATLAC TAAVFAFTQG PE SGWLAPI TLASGAAALV FGLAFLIAER NAENPVVPFA LFRERNRVAT FAAIFLAGGV LFTLTVLIGL YVQDILGYSA LRA GVGFIP FVIGMGIGLG AASQLVSRFS PRVLTIGGGY LLFGAMLYGS FFMHRGIPYF PNLVLPITIG GIGIGTIVVP LTLS AIAGV NLDRIGPASA IALMLQNLGG PLVLAVIQAV ITSRTLFLGG TTGPVKAMND EQIGALDAAY TYGLLWVAAV AVLVG AAAL FIGYTSQQVA HAQDVKDAMD AGEIEVDQPP IG

UniProtKB: Putative MFS-type transporter EfpA

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 78221
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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