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- EMDB-14495: Tail of phage SU10 genome release intermediate -

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Basic information

Entry
Database: EMDB / ID: EMD-14495
TitleTail of phage SU10 genome release intermediate
Map data
Sample
  • Virus: Escherichia phage vB_EcoP_SU10 (virus)
    • Protein or peptide: Putative structural proteinProtein
    • Protein or peptide: Putative tail fiber
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Surface proteinCell membrane
    • Protein or peptide: Portal protein
Function / homologyInvasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Putative tail fiber / Surface protein / Portal protein / Uncharacterized protein / Putative structural protein
Function and homology information
Biological speciesEscherichia phage vB_EcoP_SU10 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14495.png

Downloads & links

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Map

FileDownload / File: emd_14495.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 512 pix.
= 686.08 Å		1.34 Å/pix.
x 512 pix.
= 686.08 Å		1.34 Å/pix.
x 512 pix.
= 686.08 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.011889925 - 0.022297394
Average (Standard dev.)8.458697e-05 (±0.0007679097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 686.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14495_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_14495_half_map_2.map
Projections & Slices
AxesZYX

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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: Putative structural proteinProtein
    • Protein or peptide: Putative tail fiber
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Surface proteinCell membrane
    • 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: Yes
Host (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3.036 MDa
Virus shellShell ID: 1 / Name: Tail complex

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Macromolecule #1: Putative structural protein

MacromoleculeName: Putative structural protein / type: protein_or_peptide / ID: 1 / 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 #2: Putative tail fiber

MacromoleculeName: Putative tail fiber / type: protein_or_peptide / ID: 2 / 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 #3: Adaptor protein

MacromoleculeName: Adaptor protein / 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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 5 / 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: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / 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: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11780
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: SGD
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 8076
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7z4f:
Tail of phage SU10 genome release intermediate

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