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- EMDB-13168: SbmA-FabS11-1 in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-13168
TitleSbmA-FabS11-1 in lipid nanodisc
Map datacryoSPARC post-processed map
Sample
  • Complex: Complex of proton-driven peptide transporter SbmA with Fab S11-1
    • Protein or peptide: Proton-driven peptide transporter SbmA
Function / homology
Function and homology information


secondary active transmembrane transporter activity / microcin transmembrane transporter activity / microcin B17 transport / microcin transport / peptide transport / peptide transmembrane transporter activity / protein transport / response to antibiotic / protein homodimerization activity / ATP binding / plasma membrane
Similarity search - Function
SbmA/BacA-like / SbmA/BacA-like family / : / ABC transporter type 1, transmembrane domain superfamily
Similarity search - Domain/homology
Peptide antibiotic transporter SbmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsGhilarov D / Beis K
Funding support Poland, United Kingdom, Japan, United States, 7 items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/CC1/00274 Poland
Polish National Science Centre2019/35/D/NZ1/01770 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
Foundation for Polish ScienceTEAM/2016-3/23 Poland
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H01778X/1 United Kingdom
Japan Agency for Medical Research and Development (AMED)20am0101079 Japan
National Institutes of Health/National Cancer Institute (NIH/NCI)GM31030 United States
CitationJournal: Sci Adv / Year: 2021
Title: Molecular mechanism of SbmA, a promiscuous transporter exploited by antimicrobial peptides.
Authors: Dmitry Ghilarov / Satomi Inaba-Inoue / Piotr Stepien / Feng Qu / Elizabeth Michalczyk / Zuzanna Pakosz / Norimichi Nomura / Satoshi Ogasawara / Graham Charles Walker / Sylvie Rebuffat / So ...Authors: Dmitry Ghilarov / Satomi Inaba-Inoue / Piotr Stepien / Feng Qu / Elizabeth Michalczyk / Zuzanna Pakosz / Norimichi Nomura / Satoshi Ogasawara / Graham Charles Walker / Sylvie Rebuffat / So Iwata / Jonathan Gardiner Heddle / Konstantinos Beis /
Abstract: Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria ...Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria to multiple peptide antibiotics is controlled by the single inner membrane protein SbmA. To establish the molecular mechanism of peptide transport by SbmA and related BacA, we determined their cryo–electron microscopy structures at 3.2 and 6 Å local resolution, respectively. The structures show a previously unknown fold, defining a new class of secondary transporters named SbmA-like peptide transporters. The core domain includes conserved glutamates, which provide a pathway for proton translocation, powering transport. The structures show an outward-open conformation with a large cavity that can accommodate diverse substrates. We propose a molecular mechanism for antibacterial peptide uptake paving the way for creation of narrow-targeted therapeutics.
History
DepositionJul 4, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.418
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.418
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p34
  • Surface level: 0.418
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p34
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13168.png

Downloads & links

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Map

FileDownload / File: emd_13168.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoSPARC post-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 326.8 Å		1.02 Å/pix.
x 320 pix.
= 326.8 Å		1.02 Å/pix.
x 320 pix.
= 326.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.418 / Movie #1: 0.418
Minimum - Maximum-1.3135979 - 1.6443422
Average (Standard dev.)0.0011963767 (±0.030479504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 326.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021251.021251.02125
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z326.800326.800326.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.3141.6440.001

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Supplemental data

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Additional map: DeepEMhancer post-processed map

Fileemd_13168_additional_1.map
AnnotationDeepEMhancer post-processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map

Fileemd_13168_half_map_1.map
AnnotationHalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map

Fileemd_13168_half_map_2.map
AnnotationHalf-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 : Complex of proton-driven peptide transporter SbmA with Fab S11-1

EntireName: Complex of proton-driven peptide transporter SbmA with Fab S11-1
Components
  • Complex: Complex of proton-driven peptide transporter SbmA with Fab S11-1
    • Protein or peptide: Proton-driven peptide transporter SbmA

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Supramolecule #1: Complex of proton-driven peptide transporter SbmA with Fab S11-1

SupramoleculeName: Complex of proton-driven peptide transporter SbmA with Fab S11-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C43

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Macromolecule #1: Proton-driven peptide transporter SbmA

MacromoleculeName: Proton-driven peptide transporter SbmA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVG LFALFWFIYS PHRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI Q TALSSPHK VTIEQFYREV GVFLGIALIA VVISVLNNFF VSHYVFRWRT ...String:
MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVG LFALFWFIYS PHRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI Q TALSSPHK VTIEQFYREV GVFLGIALIA VVISVLNNFF VSHYVFRWRT AMNEYYMANW QQ LRHIEGA AQRVQEDTMR FASTLENMGV SFINAIMTLI AFLPVLVTLS AHVPELPIIG HIP YGLVIA AIVWSLMGTG LLAVVGIKLP GLEFKNQRVE AAYRKELVYG EDDATRATPP TVRE LFSAV RKNYFRLYFH YMYFNIARIL YLQVDNVFGL FLLFPSIVAG TITLGLMTQI TNVFG QVRG AFQYLINSWT TLVELMSIYK RLRSFEHELD GDKIQEVTHT LS

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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

Concentration4 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 407426
CTF correctionSoftware - Name: cryoSPARC / Software - details: Patch CTF correction
Startup modelType of model: OTHER
Details: Initial model generated by ab initio job in cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 116545
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial model generated by Buccaneer and refined by PHENIX
Output model

PDB-7p34:
Cryo-EM structure of the proton-dependent antibacterial peptide transporter SbmA-FabS11-1 in nanodiscs

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