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- EMDB-15229: T5 phage receptor-binding protein pb5 bound to ferrichrome transp... -

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Basic information

Entry
Database: EMDB / ID: EMD-15229
TitleT5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
Map dataT5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms
Sample
  • Complex: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
    • Protein or peptide: Ferrichrome outer membrane transporter/phage receptor
    • Protein or peptide: Receptor-binding protein pb5
  • Ligand: [(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
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / transmembrane transporter complex / toxic substance binding / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell ...siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / transmembrane transporter complex / 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 / symbiont entry into host cell / iron ion binding / protein domain specific binding / 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 / Receptor-binding protein pb5
Similarity search - Component
Biological speciesEscherichia phage T5 (virus) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSilale A / van den Berg B
Funding support United Kingdom, 1 items
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, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15229.png

Downloads & links

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Map

FileDownload / File: emd_15229.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 440 pix.
= 312.4 Å		0.71 Å/pix.
x 440 pix.
= 312.4 Å		0.71 Å/pix.
x 440 pix.
= 312.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.6056157 - 0.8468476
Average (Standard dev.)0.0002903852 (±0.017680341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 312.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15229_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: T5 phage receptor-binding protein pb5 bound to ferrichrome...

Fileemd_15229_half_map_1.map
AnnotationT5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms, half map 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: T5 phage receptor-binding protein pb5 bound to ferrichrome...

Fileemd_15229_half_map_2.map
AnnotationT5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms, half map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : T5 phage receptor-binding protein pb5 bound to ferrichrome transp...

EntireName: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
Components
  • Complex: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
    • Protein or peptide: Ferrichrome outer membrane transporter/phage receptor
    • Protein or peptide: Receptor-binding protein pb5
  • Ligand: [(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

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Supramolecule #1: T5 phage receptor-binding protein pb5 bound to ferrichrome transp...

SupramoleculeName: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia phage T5 (virus)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 148 KDa

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Macromolecule #1: Ferrichrome outer membrane transporter/phage receptor

MacromoleculeName: Ferrichrome outer membrane transporter/phage receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 78.816859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVEPKEDTIT VTAAPAPQES AWGPAATIAA RQSATGTKTD TPIQKVPQSI SVVTAEEMAL HQPKSVKEAL SYTPGVSVGT RGASNTYDH LIIRGFAAEG QSQNNYLNGL KLQGNFYNDA VIDPYMLERA EIMRGPVSVL YGKSSPGGLL NMVSKRPTTE P LKEVQFKA ...String:
AVEPKEDTIT VTAAPAPQES AWGPAATIAA RQSATGTKTD TPIQKVPQSI SVVTAEEMAL HQPKSVKEAL SYTPGVSVGT RGASNTYDH LIIRGFAAEG QSQNNYLNGL KLQGNFYNDA VIDPYMLERA EIMRGPVSVL YGKSSPGGLL NMVSKRPTTE P LKEVQFKA GTDSLFQTGF DFSDSLDDDG VYSYRLTGLA RSANAQQKGS EEQRYAIAPA FTWRPDDKTN FTFLSYFQNE PE TGYYGWL PKEGTVEPLP NGKRLPTDFN EGAKNNTYSR NEKMVGYSFD HEFNDTFTVR QNLRFAENKT SQNSVYGYGV CSD PANAYS KQCAALAPAD KGHYLARKYV VDDEKLQNFS VDTQLQSKFA TGDIDHTLLT GVDFMRMRND INAWFGYDDS VPLL NLYNP VNTDFDFNAK DPANSGPYRI LNKQKQTGVY VQDQAQWDKV LVTLGGRYDW ADQESLNRVA GTTDKRDDKQ FTWRG GVNY LFDNGVTPYF SYSESFEPSS QVGKDGNIFA PSKGKQYEVG VKYVPEDRPI VVTGAVYNLT KTNNLMADPE GSFFSV EGG EIRARGVEIE AKAALSASVN VVGSYTYTDA EYTTDTTYKG NTPAQVPKHM ASLWADYTFF DGPLSGLTLG TGGRYTG SS YGDPANSFKV GSYTVVDALV RYDLARVGMA GSNVALHVNN LFDREYVASC FNTYGCFWGA ERQVVATATF RF

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Macromolecule #2: Receptor-binding protein pb5

MacromoleculeName: Receptor-binding protein pb5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 69.611453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFFAGKLNN KSILSLRRGS GGDTNQHINP DSQTIFHSDM SHVIITETHS TGLRLDQGAG DYYWSEMPSR VTQLHNNDPN RVVLTEIEF SDGSRHMLSG MSMGVGAKAY GIINPQIMSQ GGLKTQITAS ADLSLDVGYF NTGTSGTIPQ KLRDGTGCQH M FGAFSGRR ...String:
MSFFAGKLNN KSILSLRRGS GGDTNQHINP DSQTIFHSDM SHVIITETHS TGLRLDQGAG DYYWSEMPSR VTQLHNNDPN RVVLTEIEF SDGSRHMLSG MSMGVGAKAY GIINPQIMSQ GGLKTQITAS ADLSLDVGYF NTGTSGTIPQ KLRDGTGCQH M FGAFSGRR GFASSAMYLG GAALYKSAWS GSGYVVADAG TLTIPSDYVR HPGARNFGFN AIYVRGRSCN RVLYGMEGPN YT TGGAVQG ASSSGALNFT YNPSNPESPK YSVGFARADP TNYAYWESMG DPNDSANGPI GIYSEHLGIY PSKITWYVTN LVY NGSGYN IDGGLFNGND IKLSPREFII KGVNVNNTSW KFINFIEKNF NVGNRADFRD VGCNLSKDSP STGISGIATF GLPT TESNN APSIKGGNVG GLHANVVSIY NFLPSASWYV SSNPPKIGNN YGDVWSENLL PLRLLGGSGS TILSGNIVFQ GNGSV HVGT VGLDLNSSRN GAIVCTMEFI DDTWLSAGGI GCFNPTEMLS QGAEYGDSRF RIGGNTINKK LHQILSLPAG EYVPFF TIK GTVVNACKLQ AAAYNPTPYW VSGLPGSVGQ TGYYTLTYYM RNDGNNNISI WLDSSMSNII GMKACLPNIK LIIQRLT HH HHHH

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Macromolecule #3: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethy...

MacromoleculeName: [(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] ...Name: [(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
type: ligand / ID: 3 / Number of copies: 1 / Formula: LU9
Molecular weightTheoretical: 1.996235 KDa
Chemical component information

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 / toxin*YM / Lipopolysaccharide

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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

Concentration8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES-NaOH
100.0 mMNaClSodium chlorideSodium chloride
0.12 %C22H42O11Decyl maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8387 / Average exposure time: 2.74 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 71476
FSC plot (resolution estimation)

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