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- PDB-7p34: Cryo-EM structure of the proton-dependent antibacterial peptide t... -

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Basic information

Entry
Database: PDB / ID: 7p34
TitleCryo-EM structure of the proton-dependent antibacterial peptide transporter SbmA-FabS11-1 in nanodiscs
ComponentsPeptide antibiotic transporter SbmA
KeywordsTRANSPORT PROTEIN / SLiPT / proton transport / peptide transport / antibiotics
Function / homology
Function and homology information


secondary active transmembrane transporter activity / microcin transmembrane transporter activity / microcin B17 transport / microcin transport / : / toxin transmembrane transporter activity / peptide transport / peptide transmembrane transporter activity / plasma membrane => GO:0005886 / ATPase-coupled transmembrane transporter activity ...secondary active transmembrane transporter activity / microcin transmembrane transporter activity / microcin B17 transport / microcin transport / : / toxin transmembrane transporter activity / peptide transport / peptide transmembrane transporter activity / plasma membrane => GO:0005886 / ATPase-coupled transmembrane transporter activity / protein transport / response to antibiotic / ATP hydrolysis 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
Chem-PGW / Peptide antibiotic transporter SbmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsGhilarov, D. / Beis, K.
Funding support United Kingdom, Japan, Poland, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H01778X/1 United Kingdom
Japan Society for the Promotion of Science (JSPS) Japan
Foundation for Polish ScienceTEAM/2016-3/23 Poland
Polish National Science Centre2016/21/B/CC1/00274 (OPUS 11) Poland
Polish National Science Centre2019/35/D/NZ1/01770 (SONATA 15) Poland
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 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct.title

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Assembly

Deposited unit
A: Peptide antibiotic transporter SbmA
B: Peptide antibiotic transporter SbmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4904
Polymers92,9922
Non-polymers1,4982
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11670 Å2
ΔGint-76 kcal/mol
Surface area38600 Å2

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Components

#1: Protein Peptide antibiotic transporter SbmA


Mass: 46496.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AFY6
#2: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of proton-driven peptide transporter SbmA with Fab S11-1
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11RELIONclassification
12cryoSPARC3.2.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 407426
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116545 / Algorithm: FOURIER SPACE / Details: The local resolution for the transporter is 3.2A / Symmetry type: POINT
Atomic model buildingDetails: Initial model generated by Buccaneer and refined by PHENIX
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066664
ELECTRON MICROSCOPYf_angle_d0.6359068
ELECTRON MICROSCOPYf_dihedral_angle_d17.269944
ELECTRON MICROSCOPYf_chiral_restr0.0441002
ELECTRON MICROSCOPYf_plane_restr0.0051100

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