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- EMDB-50995: Cryo-EM structure of SbmA in the inward-facing-wide conformation ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50995
TitleCryo-EM structure of SbmA in the inward-facing-wide conformation bound to 1 sybody
Map data
Sample
  • Complex: Peptide antibiotic transporter SbmA in complex with Sybody 2
    • Protein or peptide: Peptide antibiotic transporter SbmA
    • Protein or peptide: Peptide antibiotic transporter SbmA
    • Protein or peptide: Sybody 2
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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 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 bound to 1 sybody
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_50995.png

Downloads & links

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Map

FileDownload / File: emd_50995.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: 0.5
Minimum - Maximum-0.91536945 - 1.6484677
Average (Standard dev.)0.008980615 (±0.059271)
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_50995_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map.

Fileemd_50995_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_50995_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_50995_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 in complex with Sybody 2

EntireName: Peptide antibiotic transporter SbmA in complex with Sybody 2
Components
  • Complex: Peptide antibiotic transporter SbmA in complex with Sybody 2
    • Protein or peptide: Peptide antibiotic transporter SbmA
    • Protein or peptide: Peptide antibiotic transporter SbmA
    • Protein or peptide: Sybody 2

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Supramolecule #1: Peptide antibiotic transporter SbmA in complex with Sybody 2

SupramoleculeName: Peptide antibiotic transporter SbmA in complex with Sybody 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV SHYVFRWRTA ...String:
MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV SHYVFRWRTA MNEYYMANWQ QLRHIEGAAQ RVQEDTMRFA STLENMGVSF INAIMTLIAF LPVLVTLSAH VPELPIIGHI PYGLVIAAIV WSLMGTGLLA VVGIKLPGLE FKNQRVEAAY RKELVYGEDD ATRATPPTVR ELFSAVRKNY FRLYFHYMYF NIARILYLQV DNVFGLFLLF PSIVAGTITL GLMTQITNVF GQVRGAFQYL INSWTTLVEL MSIYKRLRSF EHELDGDKIQ EVTHTLSALE VLFQGPHHHH HHHHHH

UniProtKB: Peptide antibiotic transporter SbmA

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Macromolecule #2: Peptide antibiotic transporter SbmA

MacromoleculeName: Peptide antibiotic transporter SbmA / type: protein_or_peptide / ID: 2 / Details: Protomer B / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV SHYVFRWRTA ...String:
MSFKSFFPKP GTFFLSAFVW ALIAVIFWQA GGGDWVARIT GASGQIPISA ARFWSLDFLI FYAYYIVCVG LFALFWFIYS PHRWQYWSIL GTALIIFVTW FLVEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV SHYVFRWRTA MNEYYMANWQ QLRHIEGAAQ RVQEDTMRFA STLENMGVSF INAIMTLIAF LPVLVTLSAH VPELPIIGHI PYGLVIAAIV WSLMGTGLLA VVGIKLPGLE FKNQRVEAAY RKELVYGEDD ATRATPPTVR ELFSAVRKNY FRLYFHYMYF NIARILYLQV DNVFGLFLLF PSIVAGTITL GLMTQITNVF GQVRGAFQYL INSWTTLVEL MSIYKRLRSF EHELDGDKIQ EVTHTLSALE VLFQGPHHHH HHHHHH

UniProtKB: Peptide antibiotic transporter SbmA

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Macromolecule #3: Sybody 2

MacromoleculeName: Sybody 2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
MAGSSSQVQL VESGGGLVQA GGSLRLSCAA SGFPVIANVM YWYRQAPGKE REWVAAIDSS GEYAYYADSV KGRFTISRDN AKNTVYLQMN SLKPEDTAVY YCYVKVGSHY WGQGTQVTVS AGRAGEQRLI SEEDLNSAVD HHHHHH

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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

Concentration6.29 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: 1585 / 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: 750685
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 34724
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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