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- EMDB-54177: Cryo-EM structure of the SbmA V102G mutant variant in an expanded... -

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Basic information

Entry
Database: EMDB / ID: EMD-54177
TitleCryo-EM structure of the SbmA V102G mutant variant in an expanded outward-open conformation
Map dataSharpened map.
Sample
  • Complex: Peptide antibiotic transporter SbmA V102G
    • Protein or peptide: Peptide antibiotic transporter SbmA
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsPeptide antibiotic transporter SbmA / Peptide uptake permease (PUP) family / transmembrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


microcin transmembrane transporter activity / microcin B17 transport / microcin transport / secondary active transmembrane transporter activity / 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: 3.07 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 V102G mutant variant in an expanded outward-open conformation
Authors: Thangaratnarajah C / Ettema TW / Slotboom DJ
History
DepositionJun 25, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54177.png

Downloads & links

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Map

FileReleased
AnnotationSharpened map.
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: 1.0
Minimum - Maximum-5.5972104 - 7.5547132
Average (Standard dev.)0.00875893 (±0.14042069)
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_54177_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_54177_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_54177_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_54177_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 V102G

EntireName: Peptide antibiotic transporter SbmA V102G
Components
  • Complex: Peptide antibiotic transporter SbmA V102G
    • Protein or peptide: Peptide antibiotic transporter SbmA
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Peptide antibiotic transporter SbmA V102G

SupramoleculeName: Peptide antibiotic transporter SbmA V102G / 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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.790512 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVGL FALFWFIYSP HRWQYWSIL GTALIIFVTW FLGEVGVAVN AWYAPFYDLI QTALSSPHKV TIEQFYREVG VFLGIALIAV VISVLNNFFV S HYVFRWRT ...String:
MFKSFFPKPG TFFLSAFVWA LIAVIFWQAG GGDWVARITG ASGQIPISAA RFWSLDFLIF YAYYIVCVGL FALFWFIYSP HRWQYWSIL GTALIIFVTW FLGEVGVAVN 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 SALEVLFQGP HHHHHHHHHH

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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Macromolecule #3: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*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

Concentration5 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: 1959 / 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: 854709
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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 126495
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-9rqj:
Cryo-EM structure of the SbmA V102G mutant variant in an expanded outward-open conformation

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