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- PDB-8a8c: T5 phage receptor-binding protein pb5 bound to ferrichrome transp... -

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Basic information

Entry
Database: PDB / ID: 8a8c
TitleT5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
Components
  • Ferrichrome outer membrane transporter/phage receptor
  • Receptor-binding protein pb5
KeywordsMEMBRANE PROTEIN / Bacteriophage / receptor / TonB-dependent transporter / outer membrane
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore-iron import into cell / siderophore uptake transmembrane transporter activity / virus tail / transmembrane transporter complex / virion binding / toxic substance binding / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis ...siderophore transmembrane transport / siderophore-iron import into cell / siderophore uptake transmembrane transporter activity / virus tail / transmembrane transporter complex / virion binding / toxic substance binding / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / iron ion binding / protein domain specific binding / symbiont entry into host cell / membrane
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-LU9 / Ferrichrome outer membrane transporter/phage receptor / Receptor-binding protein pb5
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia phage T5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSilale, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural basis for host recognition and superinfection exclusion by bacteriophage T5.
Authors: Bert van den Berg / Augustinas Silale / Arnaud Baslé / Astrid F Brandner / Sophie L Mader / Syma Khalid /
Abstract: A key but poorly understood stage of the bacteriophage life cycle is the binding of phage receptor-binding proteins (RBPs) to receptors on the host cell surface, leading to injection of the phage ...A key but poorly understood stage of the bacteriophage life cycle is the binding of phage receptor-binding proteins (RBPs) to receptors on the host cell surface, leading to injection of the phage genome and, for lytic phages, host cell lysis. To prevent secondary infection by the same or a closely related phage and nonproductive phage adsorption to lysed cell fragments, superinfection exclusion (SE) proteins can prevent the binding of RBPs via modulation of the host receptor structure in ways that are also unclear. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the phage T5 outer membrane (OM) receptor FhuA in complex with the T5 RBP pb5, and the crystal structure of FhuA complexed to the OM SE lipoprotein Llp. Pb5 inserts four loops deeply into the extracellular lumen of FhuA and contacts the plug but does not cause any conformational changes in the receptor, supporting the view that DNA translocation does not occur through the lumen of OM channels. The FhuA-Llp structure reveals that Llp is periplasmic and binds to a nonnative conformation of the plug of FhuA, causing the inward folding of two extracellular loops via "reverse" allostery. The inward-folded loops of FhuA overlap with the pb5 binding site, explaining how Llp binding to FhuA abolishes further infection of by phage T5 and suggesting a mechanism for SE via the jamming of TonB-dependent transporters by small phage lipoproteins.
History
DepositionJun 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrichrome outer membrane transporter/phage receptor
B: Receptor-binding protein pb5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,4253
Polymers148,4282
Non-polymers1,9961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4260 Å2
ΔGint-22 kcal/mol
Surface area37890 Å2
MethodPISA

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Components

#1: Protein Ferrichrome outer membrane transporter/phage receptor / Ferric hydroxamate receptor / Ferric hydroxamate uptake / Ferrichrome-iron receptor


Mass: 78816.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: fhuA, tonA, b0150, JW0146 / Production host: Escherichia coli (E. coli) / References: UniProt: P06971
#2: Protein Receptor-binding protein pb5 / RBP-pb5 / Tail protein pb5


Mass: 69611.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: oad, T5.157, T5p153 / Production host: Escherichia coli (E. coli) / References: UniProt: P23207
#3: Chemical ChemComp-LU9 / [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2R,3S,4R,5R,6R)-3-oxidanyl-4-[(3S)-3-oxidanyltetradecanoyl]oxy-5-[[(3R)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate / LIPOPOLYSACCHARIDE


Mass: 1996.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C93H164N2O39P2
Has ligand of interestN
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: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.148 MDa / Experimental value: NO
Source (natural)Organism: Escherichia phage T5 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES-NaOHC8H18N2O4S1
2100 mMSodium chlorideNaCl1
30.12 %Decyl maltosideC22H42O111
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.74 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8387
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC3.3.2CTF correction
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71476 / Symmetry type: POINT

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