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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: Machin, J.M. / Mosbahi, K. / Prakaash, D. / Radford, S.E. / Walker, D. / Kalli, A.C. / Ranson, N.A.
History
DepositionJun 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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