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- PDB-8a60: Crystal structure of FhuA in complex with the superinfection excl... -

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Basic information

Entry
Database: PDB / ID: 8a60
TitleCrystal structure of FhuA in complex with the superinfection exclusion lipoprotein Llp
Components
  • Ferrichrome outer membrane transporter/phage receptor
  • Lytic conversion lipoprotein
KeywordsMEMBRANE PROTEIN / Outer membrane TonB-dependent transporter FhuA Bacteriophage T5 Superinfection exclusion E. coli
Function / homology
Function and homology information


negative regulation of receptor-mediated virion attachment to host cell / : / superinfection exclusion / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity ...negative regulation of receptor-mediated virion attachment to host cell / : / superinfection exclusion / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virion binding / toxic substance binding / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / iron ion binding / protein domain specific binding / host cell plasma membrane / membrane
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
Ferrichrome outer membrane transporter/phage receptor / Lytic conversion lipoprotein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
Authorsvan den Berg, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferrichrome outer membrane transporter/phage receptor
B: Lytic conversion lipoprotein


Theoretical massNumber of molelcules
Total (without water)88,5822
Polymers88,5822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.287, 98.287, 236.588
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 79035.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Outer menbrane transport protein for ferrichrome / 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 Lytic conversion lipoprotein


Mass: 9547.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: llp, T5.158, T5p154 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38162

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12-16% PEG 4000 0.4 M sodium isothiocyanate 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.37→85.11 Å / Num. obs: 15120 / % possible obs: 87.4 % / Redundancy: 14.4 % / CC1/2: 0.99 / Net I/σ(I): 9.2
Reflection shellResolution: 3.37→3.61 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 697 / CC1/2: 0.39 / % possible all: 48

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Processing

Software
NameVersionClassification
PHENIX(1.20rc3_4406: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY3

1by3


Resolution: 3.37→57.85 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3074 744 4.96 %
Rwork0.2532 --
obs0.2558 15002 77.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.37→57.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 0 0 5804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025951
X-RAY DIFFRACTIONf_angle_d0.5538081
X-RAY DIFFRACTIONf_dihedral_angle_d9.906815
X-RAY DIFFRACTIONf_chiral_restr0.042848
X-RAY DIFFRACTIONf_plane_restr0.0041071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.37-3.630.4369400.2974839X-RAY DIFFRACTION23
3.63-40.36611190.30152253X-RAY DIFFRACTION62
4-4.580.29441940.25663635X-RAY DIFFRACTION100
4.58-5.760.31172010.24163676X-RAY DIFFRACTION100
5.77-57.850.29061900.2453855X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.94340.21841.74731.96540.32811.21510.0679-0.1329-0.21990.24680.0012-0.5874-0.0196-0.2947-0.04050.5406-0.02340.07380.79420.16550.5598-29.614542.72946.4493
22.13190.3609-0.02690.7307-0.07492.29570.3460.0963-0.1910.1152-0.06250.17990.262-0.5508-0.25770.5518-0.1173-0.02620.90860.13760.4882-33.118343.798455.3008
31.84981.40271.07281.0336-0.1220.58820.15360.3021-0.31710.1313-0.1606-0.35270.3630.1767-0.05450.5057-0.0027-0.09930.9169-0.01530.6334-24.569530.51846.9957
40.22650.084-0.04452.23520.55422.87170.04430.8915-0.20390.2857-0.98280.58210.4414-1.15310.2122.406-1.21370.11673.6397-0.340.9144-14.399443.68619.4936
52.9588-3.5094-1.50538.6316-1.33172.94130.8462.62020.7756-1.8011-0.5180.72620.8942-0.7548-0.28590.89980.2088-0.35241.90150.29230.785-24.812758.661727.0101
67.3116-4.70444.35798.8296-3.28512.63620.68381.18130.7719-0.7134-0.80031.49740.43260.6731-0.27631.7364-0.45650.83352.5686-0.24041.4422-28.459744.098820.557
76.10374.37873.7983.19422.77422.4251-0.3303-0.06230.27370.17970.6349-0.07480.11220.6829-0.57611.18290.16780.11961.8891-0.43771.0265-24.35947.11329.4566
81.05982.82031.13868.95654.7943.3451-0.42380.01660.4443-1.8280.66381.1514-0.73630.26220.18361.08940.5811-0.23122.18240.23390.5288-29.672252.969519.0687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 131 )
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 545 )
3X-RAY DIFFRACTION3chain 'A' and (resid 546 through 714 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 35 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 62 )

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