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- PDB-9g3d: Cryo-EM structure of SbmA in the inward-facing-narrow conformatio... -

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Basic information

Entry
Database: PDB / ID: 9g3d
TitleCryo-EM structure of SbmA in the inward-facing-narrow conformation bound to 2 sybodies
Components
  • Peptide antibiotic transporter SbmA
  • Sybody 2
KeywordsTRANSPORT PROTEIN / Peptide antibiotic transporter SbmA / Peptide uptake permease (PUP) family / transmembrane 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
Chem-PGT / Peptide antibiotic transporter SbmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsThangaratnarajah, C. / Ettema, T.W. / Slotboom, D.J.
Funding support Netherlands, European Union, 4items
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 closed conformation bound to 2 sybodies
Authors: Thangaratnarajah, C. / Ettema, T.W. / Slotboom, D.J.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide antibiotic transporter SbmA
B: Peptide antibiotic transporter SbmA
C: Sybody 2
D: Sybody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3276
Polymers129,8254
Non-polymers1,5022
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Peptide antibiotic transporter SbmA


Mass: 48919.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protomer A / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sbmA, b0377, JW0368 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AFY6
#2: Antibody Sybody 2


Mass: 15992.651 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria)
#3: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: Peptide antibiotic transporter SbmA in complex with Sybody 2
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli MC1061 (bacteria)
Buffer solutionpH: 7.4 / Details: 20 mM Tris, pH 7.4, 120 mM NaCl, 0.05 % (w/v) DDM
SpecimenConc.: 6.29 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 48924 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9 sec. / Electron dose: 50.1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1585
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 60 / Used frames/image: 1-60

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.7.6particle selectionPhosaurusNet architecture
2SerialEM3.9.0 betaimage acquisition
4CTFFIND4.1.14CTF correction
7Coot0.9.8.1model fitting
9cryoSPARC3.3.2initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.23D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 750685
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71122 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038454
ELECTRON MICROSCOPYf_angle_d0.48611506
ELECTRON MICROSCOPYf_dihedral_angle_d5.4081170
ELECTRON MICROSCOPYf_chiral_restr0.0381260
ELECTRON MICROSCOPYf_plane_restr0.0041416

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