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- PDB-9rhr: FusA (ferredoxin receptor from Pectobacterium atrosepticum) in th... -

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Basic information

Entry
Database: PDB / ID: 9rhr
TitleFusA (ferredoxin receptor from Pectobacterium atrosepticum) in the presence of Ra-LPS
ComponentsFerredoxin receptor
KeywordsMEMBRANE PROTEIN / outer membrane protein / transmembrane beta-barrel / tonb-dependent transporter
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMachin, J.M. / Ranson, N.A.
Funding support United Kingdom, 2items
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: Jonathan M Machin / Khedidja Mosbahi / Dheeraj Prakaash / Sheena E Radford / Daniel Walker / Antreas C Kalli / Neil A Ranson /
Abstract: Lipopolysaccharide (LPS) is a glycolipid found uniquely in the outer membrane of diderm bacteria, formed of 4-7 acyl chains covalently linked to an extended polysaccharide chain. While a few examples ...Lipopolysaccharide (LPS) is a glycolipid found uniquely in the outer membrane of diderm bacteria, formed of 4-7 acyl chains covalently linked to an extended polysaccharide chain. While a few examples of the interaction between LPS and outer membrane proteins (OMPs) have been structurally characterised, either experimentally or computationally, the precise nature of LPS-OMP interactions and their functional consequences remains unclear. Here, we show that the addition of LPS facilitated cryoEM structure determination of FusA, a 100 kDa TonB-dependent outer membrane transporter from . A 2.8 Å structure combined with molecular dynamics of FusA with different LPS models reveals LPS binding sites with a strong LPS interaction site located adjacent to the β-seam region of the FusA β-barrel. The requirement of lipid binding for successful structure determination indicates a stabilisation of the protein, which in turn suggests a potential method for solving other, small OMPs and membrane proteins. Further, it hints at how LPS may mediate protein conformation and thus how LPS and OMPs can work in concert to maintain a structural and functional OM.
History
DepositionJun 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
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Revision 1.1Dec 24, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin receptor


Theoretical massNumber of molelcules
Total (without water)97,7871
Polymers97,7871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Presence of LPS in micelles containing FusA validated via co-elution of LPS and FusA by SEC.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ferredoxin receptor


Mass: 97786.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Gene: ECA0878 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D8U4
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: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles
Type: COMPLEX
Details: FusA protein in complex with Ra-LPS lipid solubilised in LDAO micelles. Ra-LPS added into micelles following purification
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pectobacterium atrosepticum SCRI1043 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 0.2% LDAO, 20 mM Tris-Cl (pH 8.0), 150 mM NaCl
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 30000 nm / Nominal defocus min: 9000 nm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 47.1 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2Topazparticle selection
3EPUimage acquisition
5CTFFINDCTF correction
11RELIONinitial Euler assignment
12cryoSPARCfinal Euler assignment
13RELIONclassification
14RELION43D reconstruction
15cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 754778
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84061 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Isolde and phenix real-space refine
Atomic model buildingPDB-ID: 4ZGV

4zgv


Accession code: 4ZGV / Source name: PDB / Type: experimental model

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