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- EMDB-50997: Cryo-EM structure of SbmA in the inward-facing-wide conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-50997
TitleCryo-EM structure of SbmA in the inward-facing-wide conformation
Map data
Sample
  • Complex: Peptide antibiotic transporter SbmA
    • Protein or peptide: Peptide antibiotic transporter SbmA
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsPeptide antibiotic transporter SbmA / Peptide uptake permease (PUP) family / transmembrane protein / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsThangaratnarajah C / Ettema TW / Slotboom DJ
Funding support Netherlands, European Union, 4 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.018.003 Netherlands
Netherlands Organisation for Scientific Research (NWO)024.003.019 Netherlands
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
European Union (EU)847675European Union
CitationJournal: To Be Published
Title: Cryo-EM structure of the SbmA in the inward-facing open conformation
Authors: Thangaratnarajah C / Ettema TW / Slotboom DJ
History
DepositionJul 12, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50997.png

Downloads & links

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Map

FileDownload / File: emd_50997.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 261.632 Å		1.02 Å/pix.
x 256 pix.
= 261.632 Å		1.02 Å/pix.
x 256 pix.
= 261.632 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.022 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-3.6032093 - 5.1461368
Average (Standard dev.)0.006641359 (±0.10684294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 261.632 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50997_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map.

Fileemd_50997_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 used during refinement and FSC...

Fileemd_50997_half_map_1.map
AnnotationHalf map 2 used during refinement and FSC gold-standard resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 used during refinement and FSC...

Fileemd_50997_half_map_2.map
AnnotationHalf map 1 used during refinement and FSC gold-standard resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Peptide antibiotic transporter SbmA

EntireName: Peptide antibiotic transporter SbmA
Components
  • Complex: Peptide antibiotic transporter SbmA
    • Protein or peptide: Peptide antibiotic transporter SbmA
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: Peptide antibiotic transporter SbmA

SupramoleculeName: Peptide antibiotic transporter SbmA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Peptide antibiotic transporter SbmA

MacromoleculeName: Peptide antibiotic transporter SbmA / type: protein_or_peptide / ID: 1 / Details: Protomer A and B / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.919664 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSI LGTALIIFVT WFLVEVGVAV NAWYAPFYDL IQTALSSPHK VTIEQFYREV GVFLGIALIA VVISVLNNFF V SHYVFRWR ...String:
MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSI LGTALIIFVT WFLVEVGVAV NAWYAPFYDL IQTALSSPHK VTIEQFYREV GVFLGIALIA VVISVLNNFF V SHYVFRWR TAMNEYYMAN WQQLRHIEGA AQRVQEDTMR FASTLENMGV SFINAIMTLI AFLPVLVTLS AHVPELPIIG HI PYGLVIA AIVWSLMGTG LLAVVGIKLP GLEFKNQRVE AAYRKELVYG EDDATRATPP TVRELFSAVR KNYFRLYFHY MYF NIARIL YLQVDNVFGL FLLFPSIVAG TITLGLMTQI TNVFGQVRGA FQYLINSWTT LVELMSIYKR LRSFEHELDG DKIQ EVTHT LSALEVLFQG PHHHHHHHHH H

UniProtKB: Peptide antibiotic transporter SbmA

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Macromolecule #2: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 2 / Number of copies: 2 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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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

Concentration6.4 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, pH 7.4, 120 mM NaCl, 0.05 % (w/v) DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 1620 / Average exposure time: 9.0 sec. / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 48924 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 357486
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated by the stochastic gradient decent (SGD) method.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 99732
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9g3f:
Cryo-EM structure of SbmA in the inward-facing-wide conformation

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