+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14489 | |||||||||
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Title | Bacteriophage SU10 tail and bottom part of the capsid (C1) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacteriophage / portal / VIRUS | |||||||||
Function / homology | Function and homology information Protein of unknown function DUF5309 / Family of unknown function (DUF5309) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 Similarity search - Domain/homology | |||||||||
Biological species | Escherichia phage vB_EcoP_SU10 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Siborova M / Fuzik T / Prochazkova M / Novacek J / Plevka P | |||||||||
Funding support | Czech Republic, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Tail proteins of phage SU10 reorganize into the nozzle for genome delivery. Authors: Marta Šiborová / Tibor Füzik / Michaela Procházková / Jiří Nováček / Martin Benešík / Anders S Nilsson / Pavel Plevka / Abstract: Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses ...Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses elongate upon cell attachment. Here we show that the virion of SU10 has a prolate head, containing genome and ejection proteins, and a tail, which is formed of portal, adaptor, nozzle, and tail needle proteins and decorated with long and short fibers. The binding of the long tail fibers to the receptors in the outer bacterial membrane induces the straightening of nozzle proteins and rotation of short tail fibers. After the re-arrangement, the nozzle proteins and short tail fibers alternate to form a nozzle that extends the tail by 28 nm. Subsequently, the tail needle detaches from the nozzle proteins and five types of ejection proteins are released from the SU10 head. The nozzle with the putative extension formed by the ejection proteins enables the delivery of the SU10 genome into the bacterial cytoplasm. It is likely that this mechanism of genome delivery, involving the formation of the tail nozzle, is employed by all Kuraviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14489.map.gz | 34.1 MB | EMDB map data format | |
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Header (meta data) | emd-14489-v30.xml emd-14489.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14489_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_14489.png | 118.6 KB | ||
Filedesc metadata | emd-14489.cif.gz | 7.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14489 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14489 | HTTPS FTP |
-Validation report
Summary document | emd_14489_validation.pdf.gz | 570.4 KB | Display | EMDB validaton report |
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Full document | emd_14489_full_validation.pdf.gz | 570 KB | Display | |
Data in XML | emd_14489_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_14489_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14489 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14489 | HTTPS FTP |
-Related structure data
Related structure data | 7z4aMC 7z44C 7z45C 7z46C 7z47C 7z48C 7z49C 7z4bC 7z4fC C: citing same article (ref.) M: atomic model generated by this map |
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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_14489.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Escherichia phage vB_EcoP_SU10
Entire | Name: Escherichia phage vB_EcoP_SU10 (virus) |
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Components |
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-Supramolecule #1: Escherichia phage vB_EcoP_SU10
Supramolecule | Name: Escherichia phage vB_EcoP_SU10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1519788 / Sci species name: Escherichia phage vB_EcoP_SU10 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 4.5 MDa |
-Macromolecule #1: Adaptor protein
Macromolecule | Name: Adaptor protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage vB_EcoP_SU10 (virus) |
Molecular weight | Theoretical: 28.836395 KDa |
Sequence | String: MAMPDVQYPI NTYGWLKKAV ALWADRDDDE FVNQIPNFIN FAEKEIYRNL RIPPLEKEVY LDIKDGVAYI PPDYLEAQWM MRAKDGTIF QVTSPEEISY RRQHGTINPS HWNNQPVNFA RFGSRFIFYP SIEADTPYYP DDGSPLIPAE NSVILSYYAD P PEFHEDTD ...String: MAMPDVQYPI NTYGWLKKAV ALWADRDDDE FVNQIPNFIN FAEKEIYRNL RIPPLEKEVY LDIKDGVAYI PPDYLEAQWM MRAKDGTIF QVTSPEEISY RRQHGTINPS HWNNQPVNFA RFGSRFIFYP SIEADTPYYP DDGSPLIPAE NSVILSYYAD P PEFHEDTD TSTILTIAPE LLLYFTLRHA CLFVQDDNGV QKWSALGKAI LDEMVEQNKK QEYSGSPIAI PNNMTRLQSS LP DIYGIRT SRV UniProtKB: Uncharacterized protein |
-Macromolecule #2: Surface protein
Macromolecule | Name: Surface protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage vB_EcoP_SU10 (virus) |
Molecular weight | Theoretical: 110.352617 KDa |
Sequence | String: MALYPIKSLG AVGVIADQAP TDLAPNAFTN AINARFVEQR VFKTGGNAPL SYVDEDKDLT PLSFVSMPFD YYSAGNSFLV VGTNKKLYK LTDESLTDIS RKVATVTKKA SASIKIYPVV SQIVPKESTI SMNFNQTKNL EVSLLPADAN NTNLIWEVSN S SYGSITVD ...String: MALYPIKSLG AVGVIADQAP TDLAPNAFTN AINARFVEQR VFKTGGNAPL SYVDEDKDLT PLSFVSMPFD YYSAGNSFLV VGTNKKLYK LTDESLTDIS RKVATVTKKA SASIKIYPVV SQIVPKESTI SMNFNQTKNL EVSLLPADAN NTNLIWEVSN S SYGSITVD PSDSKLATLT SFEKEGNLVV TISTANESVV AQIAVNIIDG DSGIFLSQDT VTIRKGGTTT LTAVTGKTPV TW SSNNASI VSVTPNANSL TAVITANGEG NVTITADNGT KTASCEIVSI PQIDSISLSQ SDVTVSRGSQ YILTATLSPA NAP NQNITW TSSNPNIATV SGTSTQGTIN ALLAGFTEIT ATTEEGNRVA VCTVRVDLAG RTMRTSAMAF AAPVSESVET QEEE VVTPP ESEETVYFAE PTSGIDTSGM YEGNNFYDYS NVNDIEGFAR ASLLATPLSS VTLDIVSASL DVGEEIVITA TASPE GEYS YQWSVDKTGY VSTTSVTGKS IKLVALRKGE INVTCTVSQM TQKDYDAFDD YPWYHAVISN CAVATTHYET PQVKEF ESE YFVDLPGWGE QTVVDNDGNP SVKKFNWKCE RVRSFNNRLF ALNMREANAS GVTTNYPLRL RWSNFANENK APTLWDD FA YDRVVSSDLA SNIVGQTQAL ENGYAGYIDL ADSNGSLIDI LPLKDYLFVY TEFETYIGSP TNNTYQPLMF KKLFNDSG I LAPECVVEVE GSHFVVTQND VILHNGATKK SIASNRVKNM LINEVCLVNP LATRVHLHQD KKEVWVLYVG PGEPKESFA CTKAAVWNYE FDTWSFRTIP YAQCIGLVDP PVLERGPIWS DFQEITWDDP SIKELVWRKD ATNFRQRVTI VGSFLKGFYQ VDVGALDYF YDRLNDVVIE KPLEMRLERT GIDFDNVTNE WNQKHINRFR PQTTGSGTYI FEAGGSQFSN EYGHPHTSKT Y TIGVDRHV SVRLNHPYLF YNVIDNDVNS NAAINGLTIE FAVGGRR UniProtKB: Surface protein |
-Macromolecule #3: Putative tail fiber
Macromolecule | Name: Putative tail fiber / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage vB_EcoP_SU10 (virus) |
Molecular weight | Theoretical: 83.558227 KDa |
Sequence | String: MIVYNNQAPD AVNNVGQFGA TEGSIGAYKQ AAEYAADSKY WALLAESKFG TIDDLIAEVE RLYQQGVLMK QDIEDLKQDF KDQDARLMS LIAQTNAAVS DANNAVALIN QKLIEVQNQL DVLLGMSVDV TTLPPGTPAT GSFNPNTGVI SLGIPEGEPG K DGSVKDLD ...String: MIVYNNQAPD AVNNVGQFGA TEGSIGAYKQ AAEYAADSKY WALLAESKFG TIDDLIAEVE RLYQQGVLMK QDIEDLKQDF KDQDARLMS LIAQTNAAVS DANNAVALIN QKLIEVQNQL DVLLGMSVDV TTLPPGTPAT GSFNPNTGVI SLGIPEGEPG K DGSVKDLD TAPTGVPELG DLGFYVDKDD NTVHKTTLEN IANLTPSVRS VSVNGGPALD GEVALTINKE TVGLGNVLNV AQ YSRQEIN DKFDKTTKTY QSKAEAYADA QYRQVGEKVL VWEATKYEFY TVAANKTLTP VKTEGRILTV NSRSPDSSGN IDI TIPTGN PSLYLGEMVM FPYDPSKNIS YPGVLPADGR LVSKESASDL GPSLVSGQLP VVSETEWQSG AKQYFSWGKL ADGI TDADS TNFINIRLPD WTGGEAIRAP DSDKDSQYNG SVQAQKPYVV TVNNQAPDEI TGNVNISRSI LGAASSGANS DITSL SGLT TPLSISQGGT GAKDAASARS NLGLGSVSTL DNVPIASGGT GAGDAAGARF NLGLGNSATM NTGTNSDNVL KVGDFG IGR PDGALVFDTT SQDQLLAGLD TYGLCVFRNN QQIAAPWDIW NYSSNLFFRA GDTYSMISIP FESAGKIKVF GGASGSG WK TSRTVYDTVN TTVDVNGFIK AASPIVKVFH DGSFETNEQS DGVSVKKIST GVYLISGCLG LNSDAGWGGV DGGFEIPI D RNKQPRVWLD YEVKEDGSLL IKTYHRTHST SPAFARNELE GFSDGDPVDI PKDAFISVRV EMPSK UniProtKB: Putative tail fiber |
-Macromolecule #4: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage vB_EcoP_SU10 (virus) |
Molecular weight | Theoretical: 85.055344 KDa |
Sequence | String: MAKQKYSEEV LDELRVDLQR RFNYAQGYVD MAVKGYAREA WEYFYGNLPA PVTAGSSSWV DRTVWESVNG TLQDIINVFC SGDEAVTFV ADNQQDSDAA DVATKLVNQI LLRDNPGYNI ISSAAQECLV TRNSFIKYYW DEQTSTQTEE AEGVPPEALA A YVQGLEAG ...String: MAKQKYSEEV LDELRVDLQR RFNYAQGYVD MAVKGYAREA WEYFYGNLPA PVTAGSSSWV DRTVWESVNG TLQDIINVFC SGDEAVTFV ADNQQDSDAA DVATKLVNQI LLRDNPGYNI ISSAAQECLV TRNSFIKYYW DEQTSTQTEE AEGVPPEALA A YVQGLEAG GLKNLEVFTE ENEDGTVDVK VTYEQTVKRV KVEYVPSEQI FVDEHATSFA DAQYFCHRVR RSKEDLVAMG FP KDEIEAF NDWTDTMDTT QSTVAWSRTD WRQDIDADIG TDTEDIASMV WVYEHYIRTG VLDKNKESKL YQVIQAGEHI LHT EEVTHI PFVTFCPYPI PGSFYGQSVY DITKDIQDLR TALVRGYIDN VNNANYGRYK ALVGAYDRRS LLDNRPGGVV EMER QDAID LFPYHNLPQG IDGLLGMSEE LKETRTGVTK LGMGINPDVF KNDNAYATVG LMMNAAQNRL RMVCRNIAHN GMVEL MRGI YNLIRENGEV PIEVQTPRGM IQVNPKQLPA RHNLQVVVAI SPNEKAERAQ KLISLKQLIA ADAQLAPLFG LEQDRY MTA QIFELMGIKD THKYLLPLEQ YQPPEPSPME ILQLEMTKAQ VENVQASSQK MIADAFDQRE RTTFEQQKAA DELSLRQ EE LQFKQENAAD AMTLENRKED NNATLEQAKH KLALMQQQVR QYESVLKELQ MVMSHQVDQE KIVQQARVQD KTLELQKK E ANVTKKEQQA SLKDSRIPGK RLGSKK UniProtKB: Portal protein |
-Macromolecule #5: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 5 / Number of copies: 17 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage vB_EcoP_SU10 (virus) |
Molecular weight | Theoretical: 38.616457 KDa |
Sequence | String: MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQTIFSWQ TDALASVDGN NAHVEGSRAE DGEMKPTVIK SNVTQILRK VVRVSDTANT TANYGRGREL MYQLEKKGKE IKRDLEKILL SGQARTDVLA DQYLTNSAAD PAVAGLNDTH A ARKTGAFQ ...String: MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQTIFSWQ TDALASVDGN NAHVEGSRAE DGEMKPTVIK SNVTQILRK VVRVSDTANT TANYGRGREL MYQLEKKGKE IKRDLEKILL SGQARTDVLA DQYLTNSAAD PAVAGLNDTH A ARKTGAFQ FLCAHGGLAG GVVDKTKNGP ADPDTGAVTV KVAQNASNPT TNIGFDEADI FDMTLQLYTA GSEADIIMIN PA HAKIFAG LQENTQGSRK RIFENTKQFI YEVNSITDPL GQSYKIIVNR WMPTDAVYFF RSADWTQMVL RAPKRTELAK DGS YEKWMI EMEVGLRHRN PYASGVLFTA AGKAAA UniProtKB: Major head protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | PFU 10^11 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7z4a: |