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- EMDB-51036: CryoEM structure of the proton-dependent antibacterial peptide tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-51036
TitleCryoEM structure of the proton-dependent antibacterial peptide transporter SbmA in complex with FabS11-1 in lipid nanodiscs at pH 5.5, inward-open state
Map data
Sample
  • Complex: A dimer of SbmA bound to a single FabS11-1
    • Complex: SbmA dimer
      • Protein or peptide: Peptide antibiotic transporter SbmA
    • Complex: Single FabS11-1
      • Protein or peptide: 11-1 FabH
      • Protein or peptide: 11-1 FabL
KeywordsSLiPT / antimicrobial peptide / microcin / TRANSPORT PROTEIN
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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsGhilarov D / Beis K
Funding support United Kingdom, European Union, 4 items
OrganizationGrant numberCountry
Wellcome Trust221868/Z/20/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H01778X/1 United Kingdom
European Regional Development FundTEAM/2016-3/23European Union
CitationJournal: To Be Published
Title: Structure and mechanism of SLiPT transporters
Authors: Ettema TW / Thangaratnarajah C / Inaba-Inoue S
History
DepositionJul 15, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51036.png

Downloads & links

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Map

FileDownload / File: emd_51036.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.33395052 - 0.5884555
Average (Standard dev.)0.00020215512 (±0.012162688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51036_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_51036_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 : A dimer of SbmA bound to a single FabS11-1

EntireName: A dimer of SbmA bound to a single FabS11-1
Components
  • Complex: A dimer of SbmA bound to a single FabS11-1
    • Complex: SbmA dimer
      • Protein or peptide: Peptide antibiotic transporter SbmA
    • Complex: Single FabS11-1
      • Protein or peptide: 11-1 FabH
      • Protein or peptide: 11-1 FabL

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Supramolecule #1: A dimer of SbmA bound to a single FabS11-1

SupramoleculeName: A dimer of SbmA bound to a single FabS11-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SbmA dimer

SupramoleculeName: SbmA dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Single FabS11-1

SupramoleculeName: Single FabS11-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: 11-1 FabH

MacromoleculeName: 11-1 FabH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.932156 KDa
SequenceString: LKLLDSGAEL VKPGASVKLS CTASGFNIKD TYMYWVKQRP DQGLEWIGRI DPANGNSKYD PKFQGKATIT ADTSSNTAYL QVSSLTSED TAVYYCARWL VRGRRGTMDY WGQGTSVTVS SAKTTAPSVY PLAPVCGDTT GSSVTLGCLV KGYFPEPVTL T WNSGSLSS ...String:
LKLLDSGAEL VKPGASVKLS CTASGFNIKD TYMYWVKQRP DQGLEWIGRI DPANGNSKYD PKFQGKATIT ADTSSNTAYL QVSSLTSED TAVYYCARWL VRGRRGTMDY WGQGTSVTVS SAKTTAPSVY PLAPVCGDTT GSSVTLGCLV KGYFPEPVTL T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PRGPTIKPCP PCKCP

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Macromolecule #2: 11-1 FabL

MacromoleculeName: 11-1 FabL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.318711 KDa
SequenceString: DIVMTQSPAI LSASPGEKVT MTCRASSSVS YMHWYQQKPG SSPKPWIYAT SNLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPRTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
DIVMTQSPAI LSASPGEKVT MTCRASSSVS YMHWYQQKPG SSPKPWIYAT SNLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPRTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #3: Peptide antibiotic transporter SbmA

MacromoleculeName: Peptide antibiotic transporter SbmA / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 46.496039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVGL FALFWFIYSP HRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV S HYVFRWRT ...String:
MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVGL FALFWFIYSP HRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV S HYVFRWRT AMNEYYMANW QQLRHIEGAA QRVQEDTMRF ASTLENMGVS FINAIMTLIA FLPVLVTLSA HVPELPIIGH IP YGLVIAA IVWSLMGTGL LAVVGIKLPG LEFKNQRVEA AYRKELVYGE DDATRATPPT VRELFSAVRK NYFRLYFHYM YFN IARILY LQVDNVFGLF LLFPSIVAGT ITLGLMTQIT NVFGQVRGAF QYLINSWTTL VELMSIYKRL RSFEHELDGD KIQE VTHTL S

UniProtKB: Peptide antibiotic transporter SbmA

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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

Concentration5 mg/mL
BufferpH: 5.5 / Component - Concentration: 20.0 mM / Component - Name: MES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / 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: 42.39 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 / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56582
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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