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- EMDB-13175: Peptide transporter BacA in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-13175
TitlePeptide transporter BacA in lipid nanodisc
Map datacryoSPARC post-processed map
Sample
  • Complex: Peptide transporter BacA in lipid nanodisc
    • Protein or peptide: Peptide transporter BacA
Function / homologySbmA/BacA-like / SbmA/BacA-like family / : / peptide transport / peptide transmembrane transporter activity / ABC transporter type 1, transmembrane domain superfamily / ATP binding / plasma membrane / Bacteroid development protein BacA
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.36 Å
AuthorsGhilarov D / Beis K
Funding support Poland, United Kingdom, Japan, United States, 6 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/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 6, 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: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13175.png

Downloads & links

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Map

FileDownload / File: emd_13175.map.gz / Format: CCP4 / Size: 15.6 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.)
1.69 Å/pix.
x 160 pix.
= 270.4 Å		1.69 Å/pix.
x 160 pix.
= 270.4 Å		1.69 Å/pix.
x 160 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.406291 - 2.7728808
Average (Standard dev.)0.0006176533 (±0.08503729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 270.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z270.400270.400270.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.4062.7730.001

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Supplemental data

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Sample components

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Entire : Peptide transporter BacA in lipid nanodisc

EntireName: Peptide transporter BacA in lipid nanodisc
Components
  • Complex: Peptide transporter BacA in lipid nanodisc
    • Protein or peptide: Peptide transporter BacA

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Supramolecule #1: Peptide transporter BacA in lipid nanodisc

SupramoleculeName: Peptide transporter BacA in lipid nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Peptide transporter BacA

MacromoleculeName: Peptide transporter BacA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFQSFFPKPK LFFISSAVWS LLAVLAWYAG GRDIGAYLGL PPLPPGQEPV IGVSVFWSTP FLWFYIYYA VVAGLFAAFW FAYSPHRWQY WSVLGTALII FNTYFSVQVS VAINAWYGPF Y DLIQQALA RTAPVTAGQL YSGMIGFSGI AFVAVTVGVL NLFFVSHYIF ...String:
MFQSFFPKPK LFFISSAVWS LLAVLAWYAG GRDIGAYLGL PPLPPGQEPV IGVSVFWSTP FLWFYIYYA VVAGLFAAFW FAYSPHRWQY WSVLGTALII FNTYFSVQVS VAINAWYGPF Y DLIQQALA RTAPVTAGQL YSGMIGFSGI AFVAVTVGVL NLFFVSHYIF RWRTAMNEFY VA HWPRLRH VEGASQRVQE DTMRFSSTVE RLGVGLVSSI MTLIAFLPVL FKFSEQVNVL PIV GEIPHA LVWAAVFWSV FGTVFLAAVG IKLPGLEFRN QRVEAAYRKE LVYGEDHEDR ADPI TLAQL FDNVRRNYFR LYFHYMYFNI ARIFYLQADN LFGTFVLVPA IVAGKLTLGV MNQVL NVFG QVRESFQYLV NSWTTIVELL SIYKRLKAFE SVLVDEPLPE IDRQFIDAGG KEELAL

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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: 7.5
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: 405208
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) / Resolution.type: BY AUTHOR / Resolution: 6.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 17648
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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