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Yorodumi- EMDB-15229: T5 phage receptor-binding protein pb5 bound to ferrichrome transp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15229 | |||||||||
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Title | T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA | |||||||||
Map data | T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms | |||||||||
Sample |
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Function / homology | Function and homology information siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virus tail / virion binding / toxic substance binding / transmembrane transporter complex / 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 / toxic substance binding / transmembrane transporter complex / 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 | |||||||||
Biological species | Escherichia phage T5 (virus) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Silale A / van den Berg B | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15229.map.gz | 306.9 MB | EMDB map data format | |
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Header (meta data) | emd-15229-v30.xml emd-15229.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15229_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_15229.png | 45.9 KB | ||
Masks | emd_15229_msk_1.map | 325 MB | Mask map | |
Others | emd_15229_half_map_1.map.gz emd_15229_half_map_2.map.gz | 301.5 MB 301.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15229 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15229 | HTTPS FTP |
-Validation report
Summary document | emd_15229_validation.pdf.gz | 926.2 KB | Display | EMDB validaton report |
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Full document | emd_15229_full_validation.pdf.gz | 925.7 KB | Display | |
Data in XML | emd_15229_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | emd_15229_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15229 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15229 | HTTPS FTP |
-Related structure data
Related structure data | 8a8cMC 8a60C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15229.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.71 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15229_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: T5 phage receptor-binding protein pb5 bound to ferrichrome...
File | emd_15229_half_map_1.map | ||||||||||||
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Annotation | T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: T5 phage receptor-binding protein pb5 bound to ferrichrome...
File | emd_15229_half_map_2.map | ||||||||||||
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Annotation | T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA at 3.1 angstroms, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T5 phage receptor-binding protein pb5 bound to ferrichrome transp...
Entire | Name: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA |
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Components |
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-Supramolecule #1: T5 phage receptor-binding protein pb5 bound to ferrichrome transp...
Supramolecule | Name: T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia phage T5 (virus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 148 KDa |
-Macromolecule #1: Ferrichrome outer membrane transporter/phage receptor
Macromolecule | Name: Ferrichrome outer membrane transporter/phage receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 78.816859 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Receptor-binding protein pb5
Macromolecule | Name: Receptor-binding protein pb5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage T5 (virus) |
Molecular weight | Theoretical: 69.611453 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #3: [(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethy...
Macromolecule | 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] ...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 |
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Molecular weight | Theoretical: 1.996235 KDa |
Chemical component information | ChemComp-LU9: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |