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- EMDB-14492: Bacteriophage SU10 virion (C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-14492
TitleBacteriophage SU10 virion (C1)
Map data
Sample
  • Virus: Escherichia phage vB_EcoP_SU10 (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: Putative structural proteinProtein
    • Protein or peptide: AdaptorAdapter
    • Protein or peptide: Surface proteinCell membrane
    • Protein or peptide: Putative tail fiber
    • Protein or peptide: Putative tail tip fiber protein
    • Protein or peptide: Portal protein
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
Putative tail fiber / Surface protein / Putative tail tip fiber protein / Major head protein / Portal protein / Uncharacterized protein / Putative structural protein
Similarity search - Component
Biological speciesEscherichia phage vB_EcoP_SU10 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsSiborova M / Fuzik T / Prochazkova M / Novacek J / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLL1906 Czech Republic
CitationJournal: 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
DepositionMar 3, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14492.png

Downloads & links

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Map

FileDownload / File: emd_14492.map.gz / Format: CCP4 / Size: 8.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.07505663 - 0.12993701
Average (Standard dev.)0.000572568 (±0.0045428597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions129612961296
Spacing129612961296
CellA=B=C: 1788.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14492_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14492_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage vB_EcoP_SU10

EntireName: Escherichia phage vB_EcoP_SU10 (virus)
Components
  • Virus: Escherichia phage vB_EcoP_SU10 (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: Putative structural proteinProtein
    • Protein or peptide: AdaptorAdapter
    • Protein or peptide: Surface proteinCell membrane
    • Protein or peptide: Putative tail fiber
    • Protein or peptide: Putative tail tip fiber protein
    • Protein or peptide: Portal protein

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Supramolecule #1: Escherichia phage vB_EcoP_SU10

SupramoleculeName: 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
Host (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 32 MDa

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Macromolecule #1: Major head protein

MacromoleculeName: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 95 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 38.616457 KDa
SequenceString: 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

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Macromolecule #2: Putative structural protein

MacromoleculeName: Putative structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 29.258613 KDa
SequenceString: MAIETNAVVI TDLNPLYPRD RDYIYEGAAQ IRLIKQTLQN TFPNVTEPVD IDSDTFKIMS EKLKFTGDAM DVGGLMIKNV TPGTGDKDV VTKGQMEAFM KNWMENKLYR IGSYYITEED INPGDSISLG FGSWAKVTGV IMGTGVVNPD GSVPNAQRVE F QAGGTGGR ...String:
MAIETNAVVI TDLNPLYPRD RDYIYEGAAQ IRLIKQTLQN TFPNVTEPVD IDSDTFKIMS EKLKFTGDAM DVGGLMIKNV TPGTGDKDV VTKGQMEAFM KNWMENKLYR IGSYYITEED INPGDSISLG FGSWAKVTGV IMGTGVVNPD GSVPNAQRVE F QAGGTGGR VFNTIRTENV PLMTVNGSSF SLSSNTHSHN MVFGRGDASG HNSSPNWYSP GGGYSQRTDN DTHTHTISGS VS LGRDDIS RQPINTLPPF RAAHIWRRIS

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Macromolecule #3: Adaptor

MacromoleculeName: Adaptor / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 28.836395 KDa
SequenceString: 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

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Macromolecule #4: Surface protein

MacromoleculeName: Surface protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 110.352617 KDa
SequenceString: 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

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Macromolecule #5: Putative tail fiber

MacromoleculeName: Putative tail fiber / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 83.558227 KDa
SequenceString: 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

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Macromolecule #6: Putative tail tip fiber protein

MacromoleculeName: Putative tail tip fiber protein / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 35.30393 KDa
SequenceString: MGAGGFRKNT GRNNTTLPYN VGFLNNVQDT ETYNVAVYDE LQKVSTATNQ MFQAIDEIHE EIDVRIKALN AMNLQFDELE NRITTEIET AIADIQTQMG NLSTEDIWDN SVQPPVKLES TVSGFKTSIE GNTTKIQTVE GIVNDQGQEI ALVQTELQNI N GSLSQYMK ...String:
MGAGGFRKNT GRNNTTLPYN VGFLNNVQDT ETYNVAVYDE LQKVSTATNQ MFQAIDEIHE EIDVRIKALN AMNLQFDELE NRITTEIET AIADIQTQMG NLSTEDIWDN SVQPPVKLES TVSGFKTSIE GNTTKIQTVE GIVNDQGQEI ALVQTELQNI N GSLSQYMK LSEYEATWGV NSTVNGRYAG VKLTNNGTNS QFQVTANKFI VGDGSSGNTP FVFEGGRARM EFADIKNVNI TT AQIANAR IQWAQIDNVS ISNAQIQNLS ADKITAGSMW GSNWRLTVGG DFVMGGTGGA QLWMNGNRID FYDGSGALRI RIG SW

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Macromolecule #7: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 85.055344 KDa
SequenceString: 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

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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

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTristris
10.0 mMNaClSodium chloridesodium chloride
10.0 mMCaCl2calcium chloride
GridModel: 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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsPFU 10^11

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11780
Startup modelType of model: OTHER / Details: SGD
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 9418
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7z4b:
Bacteriophage SU10 virion (C1)

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