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- EMDB-14873: Tail tip of siphophage T5 : open cone after interaction with bact... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Tail tip of siphophage T5 : open cone after interaction with bacterial receptor FhuA | |||||||||
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![]() | Bacteriophage / Siphophage / T5 / baseplate / VIRAL PROTEIN | |||||||||
Function / homology | ![]() peptidoglycan muralytic activity / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / viral tail assembly / cytolysis / metabolic process / virus tail / symbiont entry into host / symbiont genome entry into host cell via pore formation in plasma membrane / defense response to bacterium Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Linares R / Arnaud CA / Effantin G / Darnault C / Epalle N / Boeri Erba E / Schoehn G / Breyton C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of bacteriophage T5 infection trigger and cell wall perforation. Authors: Romain Linares / Charles-Adrien Arnaud / Grégory Effantin / Claudine Darnault / Nathan Hugo Epalle / Elisabetta Boeri Erba / Guy Schoehn / Cécile Breyton / ![]() Abstract: Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a ...Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a long flexible tail () at the tip of which receptor binding proteins (RBPs) specifically interact with their host, triggering infection. In siphophage T5, the unique RBP is located at the extremity of a central fiber. We present the structures of T5 tail tip, determined by cryo-electron microscopy before and after interaction with its receptor, FhuA, reconstituted into nanodisc. These structures bring out the important conformational changes undergone by T5 tail tip upon infection, which include bending of T5 central fiber on the side of the tail tip, tail anchoring to the membrane, tail tube opening, and formation of a transmembrane channel. The data allow to detail the first steps of an otherwise undescribed infection mechanism. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.1 KB 23.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.7 KB | Display | ![]() |
Images | ![]() | 127.4 KB | ||
Masks | ![]() | 15.6 MB | ![]() | |
Others | ![]() ![]() ![]() | 11.9 MB 11.9 MB 11.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zqpMC ![]() 7qg9C ![]() 7zhjC ![]() 7zlvC ![]() 7zn2C ![]() 7zn4C ![]() 7zqbC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.351 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: #1
File | emd_14873_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_14873_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_14873_half_map_2.map | ||||||||||||
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Sample components
-Entire : Escherichia virus T5
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Escherichia virus T5
Supramolecule | Name: Escherichia virus T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d, incubated with E. coli receptor FhuA reconstituted into nanodisc NCBI-ID: 2695836 / Sci species name: Escherichia virus T5 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Probable baseplate hub protein
Macromolecule | Name: Probable baseplate hub protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 107.279766 KDa |
Sequence | String: MKKILDSAKN YLNTHDKLKT ACLIALELPS SSGSAATYIY LTDYFRDVTY NGILYRSGKV KSISSHKQNR QLSIGSLSFT ITGTAEDEV LKLVQNGVSF LDRGITIHQA IINEEGNILP VDPDTDGPLL FFRGRITGGG IKDNVNTSGI GTSVITWNCS N QFYDFDRV ...String: MKKILDSAKN YLNTHDKLKT ACLIALELPS SSGSAATYIY LTDYFRDVTY NGILYRSGKV KSISSHKQNR QLSIGSLSFT ITGTAEDEV LKLVQNGVSF LDRGITIHQA IINEEGNILP VDPDTDGPLL FFRGRITGGG IKDNVNTSGI GTSVITWNCS N QFYDFDRV NGRYTDDASH RGLEVVNGTL QPSNGAKRPE YQEDYGFFHS NKSTTILAKY QVKEERYKLQ SKKKLFGLSR SY SLKKYYE TVTKEVDLDF NLAAKFIPVV YGVQKIPGIP IFADTELNNP NIVYVVYAFA EGEIDGFLDF YIGDSPMICF DET DSDTRT CFGRKKIVGD TMHRLAAGTS TSQPSVHGQE YKYNDGNGDI RIWTFHGKPD QTAAQVLVDI AKKKGFYLQN QNGN GPEYW DSRYKLLDTA YAIVRFTINE NRTEIPEISA EVQGKKVKVY NSDGTIKADK TSLNGIWQLM DYLTSDRYGA DITLD QFPL QKVISEAKIL DIIDESYQTS WQPYWRYVGW NDPLSENRQI VQLNTILDTS ESVFKNVQGI LESFGGAINN LSGEYR ITV EKYSTNPLRI NFLDTYGDLD LSDTTGRNKF NSVQASLVDP ALSWKTNSIT FYNSKFKEQD KGLDKKLQLS FANITNY YT ARSYADRELK KSRYSRTLSF SVPYKFIGIE PNDPIAFTYE RYGWKDKFFL VDEVENTRDG KINLVLQEYG EDVFINSE Q VDNSGNDIPD ISNNVLPPRD FKYTPTPGGV VGAIGKNGEL SWLPSLTNNV VYYSIAHSGH VNPYIVQQLE NNPNERMIQ EIIGEPAGLA IFELRAVDIN GRRSSPVTLS VDLNSAKNLS VVSNFRVVNT ASGDVTEFVG PDVKLAWDKI PEEEIIPEIY YTLEIYDSQ DRMLRSVRIE DVYTYDYLLT YNKADFALLN SGALGINRKL RFRIRAEGEN GEQSVGWATI |
-Macromolecule #2: Probable tape measure protein
Macromolecule | Name: Probable tape measure protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 131.639578 KDa |
Sequence | String: MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP RTLYSIERAA DRAAKSLTKM QASRGMAGIT KSIDGIGDK LDYLAIQLIE VTDKLEIGFD GVSRSVKAMG NDVAAATEKV QDRLYDTNRA LGGTSKGFND TAGAAGRASR A LGNTSGSA ...String: MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP RTLYSIERAA DRAAKSLTKM QASRGMAGIT KSIDGIGDK LDYLAIQLIE VTDKLEIGFD GVSRSVKAMG NDVAAATEKV QDRLYDTNRA LGGTSKGFND TAGAAGRASR A LGNTSGSA RGATRDFAAM AKIGGRLPIM YAALASNVFV LQTAFESLKV GDQLNRLEQF GTIVGTMTGT PVQTLALSLQ NA TNGAISF EEAMRQASSA SAYGFDSEQL EQFGLVARRA AAVLGVDMTD ALNRVIKGVS KQEIELLDEL GVTIRLNDAY ENY VKQLNA TSTGIKYTVD SLTTYQKQQA YANEVIAEST RRFGYLDDAL KATSWEQFAA NANSALRSLQ QSAATYLNPV MDTL NTFLY QTKSSQMRVS AMARSASAKT TPAENVTALI ENAVGAREDL DTYLKESEER VKKAQELKQQ LDDLKAKQAA TAPIA NALT AGGIGGDESN KLVVQLTNEL ARQNKEIEER TKTEKVLRQA VQDTGEALLR NGKLAEQLGA KMKYADTAVP GDKGVF EVD PNNLKAVSEI QKNFDFLKKS SSDTANNIRM AASSITNAKK ASSDLNSVVK AVEDTSKVTG QSADTLVKNL NLGFSSL DQ MKAAQKGLSE YVTAMDKSEQ NALEVAKRKD EVYNQTKDKA KAEAAAREVL LRQQQEQLTA AKALLAINPN DPEALKQV A KIETEILNTK AQGFENAKKT KDYTDKILGV DREIALLNDR TMTSTQYRLA QLRLELQLEQ EKTELYSKQA DGQAKVEQS RRAQAQISRE IWEAEKQGTA SHVSALMDAL EVSQTQRNVT GQSQILTERL SILQQQLELS KGNTEEELKY RNEIYKTSAA LEQLKKQRE SQMQQQVGSS VGATYTPTTG LIGEDKDFAD MQNRMASYDQ AISKLSELNS EATAVAQSMG NLTNAMIQFS Q GSLDTTSM IASGMQTVAS MIQYSTSQQV SAIDQAIAAE QKRDGKSEAS KAKLKKLEAE KLKIQQDAAK KQIIIQTAVA VM QAATAVP YPFSIPLMVA AGLAGALALA QASSASGMSS IADSGADTTQ YLTLGERQKN VDVSMQASSG ELSYLRGDKG IGN ANSFVP RAEGGMMYPG VSYQMGEHGT EVVTPMVPMK ATPNDQLSDG SKTTSGRPII LNISTMDAAS FRDFASNNST AFRD AVELA LNENGTTLKS LGNS |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: intensity 25 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV Details: 3 uL of T5 tails sample (with or without FhuA-ND) were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot ...Details: 3 uL of T5 tails sample (with or without FhuA-ND) were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent humidity, 20 Celsius degrees, 5 s blotting time, blot force 0). | |||||||||||||||
Details | Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d, incubated with E. coli receptor FhuA reconstituted into nanodisc |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-7zqp: |