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- EMDB-53974: FusA (ferredoxin receptor from Pectobacterium atrosepticum) in th... -

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Basic information

Entry
Database: EMDB / ID: EMD-53974
TitleFusA (ferredoxin receptor from Pectobacterium atrosepticum) in the presence of Ra-LPS
Map dataMasked postprocessed map, generated in RELION
Sample
  • Complex: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles
    • Protein or peptide: Ferredoxin receptor
Keywordsouter membrane protein / transmembrane beta-barrel / tonb-dependent transporter / MEMBRANE PROTEIN
Function / homologyTonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / cell outer membrane / TonB-dependent receptor plug domain-containing protein
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMachin JM / Ranson NA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: J Struct Biol X / Year: 2025
Title: The structure of the bacterial outer membrane transporter FusA enabled by addition of the native lipid lipopolysaccharide
Authors: Machin JM / Mosbahi K / Prakaash D / Radford SE / Walker D / Kalli AC / Ranson NA
History
DepositionJun 10, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53974.png

Downloads & links

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Map

FileDownload / File: emd_53974.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked postprocessed map, generated in RELION
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 400 pix.
= 364. Å		0.91 Å/pix.
x 400 pix.
= 364. Å		0.91 Å/pix.
x 400 pix.
= 364. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.6306091 - 1.3565966
Average (Standard dev.)0.00040494246 (±0.014714975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 364.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53974_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: Tightly masked map for resolving fine detail in...

Fileemd_53974_additional_1.map
AnnotationTightly masked map for resolving fine detail in the core of the protein. Used to make closeups in Figure 3. Postprocessed in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked postprocessed map, generated in RELION

Fileemd_53974_additional_2.map
AnnotationUnmasked postprocessed map, generated in RELION
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, generated in cryoSPARC Non-Uniform refine

Fileemd_53974_half_map_1.map
AnnotationHalf-map 2, generated in cryoSPARC Non-Uniform refine
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1, generated in cryoSPARC Non-Uniform refine

Fileemd_53974_half_map_2.map
AnnotationHalf-map 1, generated in cryoSPARC Non-Uniform refine
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles

EntireName: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles
Components
  • Complex: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles
    • Protein or peptide: Ferredoxin receptor

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Supramolecule #1: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles

SupramoleculeName: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles. Ra-LPS added into micelles following purification
Source (natural)Organism: Pectobacterium atrosepticum SCRI1043 (bacteria)

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Macromolecule #1: Ferredoxin receptor

MacromoleculeName: Ferredoxin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium atrosepticum SCRI1043 (bacteria)
Molecular weightTheoretical: 97.786562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MQQNDTSADE NQQKNNAESE EEQQGDSSSG NSEDTILVRS TPTSQSMGMQ IINAEQIKKM PTGNGSVTE LLKNNPNVQF SNTASSSNIP GELAPENVSF HGEKFYNNNF MVDGLSNNNN INPGANNGEL NQQPDGYSPA D LPAGGPQS ...String:
MGSSHHHHHH SSGLVPRGSH MQQNDTSADE NQQKNNAESE EEQQGDSSSG NSEDTILVRS TPTSQSMGMQ IINAEQIKKM PTGNGSVTE LLKNNPNVQF SNTASSSNIP GELAPENVSF HGEKFYNNNF MVDGLSNNNN INPGANNGEL NQQPDGYSPA D LPAGGPQS FWINSELIES LEVFDSNISA KYGDFTGGVV DAKTMDPKLD KSSGKISYRT TRDSWTKYHI SEVISEEFYS GT NLYYQPK FKKHFYSATF NQPLSDKAGF IFAYNRQQSD IPYYHEYLQQ WDDQERINET YLLKGTYLTD SGDIIRMTGM YSP HESKFY KKDVKNGGFT NSGGGYRFNM EWEHNASWGK MTSLAGYQYT EDKTEHEADS YQTWRRFSSG FVSNVIDWSS SGGA NGQNS NIGGYGSFAT NTSSFSLKQD YELNPVSWYG INHQIDFGWE TDFYTSRYRR FSDVYTGGVL VVPTGASAGS VVCQS GDEL CIPGEQYSRT RILYPERNVQ VSNVNYAAYL QNSMSYGRLE VTPGVRVSYD DFLENLNIAP RFSASYDVFG DRSTRL FGG ANRYYAGNIL AYKMRQGIGS NIQESRISPT APWTTPTLRT GTNYNVSDLN TPYSDELSLG LSQRVMSTVW TAKWVNR QG KEQFGRETTT IDGQSYRVMN NKGHTEGNTF SLEVEPISPH RFSFAEVNWK LGASVTKNKS NSIYYYDSAN QDEQRVIF D DKLMYRGDID AMNFNTPWRA FLNVNTYFPA VRLSWDQRVG YTAGYKGYTT SSIQVQCPGG SSACNGDPSF VGGATEYFP TQYDDFISYD WRFSYSQPVY KTQTLDITLD VLNVLDNVVE TNQTGTSNKP IVIYKPGRQF WLGVAYTW

UniProtKB: TonB-dependent receptor plug domain-containing protein

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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

Concentration10 mg/mL
BufferpH: 8 / Details: 0.2% LDAO, 20 mM Tris-Cl (pH 8.0), 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 47.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 30.0 µm / Nominal defocus min: 9.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 754778
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 4.0), cryoSPARC (ver. 3)) / Number images used: 84061
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Via cryoSPARC Non-Uniform refinement
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4zgv


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsIsolde and phenix real-space refine
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9rhr:
FusA (ferredoxin receptor from Pectobacterium atrosepticum) in the presence of Ra-LPS

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