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- EMDB-60750: Structure of the bacteriophage T5 tail tip complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60750
TitleStructure of the bacteriophage T5 tail tip complex
Map data
Sample
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Baseplate tube protein p140
    • Protein or peptide: Distal tail protein pb9
    • Protein or peptide: Baseplate hub protein pb3
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, baseplate / virus tail
Similarity search - Function
: / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain
Similarity search - Domain/homology
Baseplate tube protein p140 / Distal tail protein pb9 / Baseplate hub protein pb3
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPeng YN / Liu HR
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structures of Mature and Urea-Treated Empty Bacteriophage T5: Insights into Siphophage Infection and DNA Ejection.
Authors: Yuning Peng / Huanrong Tang / Hao Xiao / Wenyuan Chen / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, ...T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, we used cryo-electron microscopy (cryo-EM) to determine the structures of mature T5 (a laboratory-adapted, fiberless T5 mutant) and urea-treated empty T5 (lacking the tip complex) at near-atomic resolutions. Atomic models of the head, connector complex, tail tube, and tail tip were built for mature T5, and atomic models of the connector complex, comprising the portal protein pb7, adaptor protein p144, and tail terminator protein p142, were built for urea-treated empty T5. Our findings revealed that the aforementioned proteins did not undergo global conformational changes before and after DNA ejection, indicating that these structural features were conserved among most myophages and siphophages. The present study elucidates the underlying mechanisms of siphophage infection and DNA ejection.
History
DepositionJul 10, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60750.png

Downloads & links

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Map

FileDownload / File: emd_60750.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.093823895 - 0.12418054
Average (Standard dev.)0.0002569819 (±0.0070309183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60750_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_60750_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 T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Baseplate tube protein p140
    • Protein or peptide: Distal tail protein pb9
    • Protein or peptide: Baseplate hub protein pb3

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Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2695836 / Sci species name: Escherichia phage T5 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Baseplate tube protein p140

MacromoleculeName: Baseplate tube protein p140 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 34.367605 KDa
SequenceString: MFYSLMRESK IVIEYDGRGY HFDALSNYDA STSFQEFKTL RRTIHNRTNY ADSIINAQDP SSISLAINFS TTLIESNFFD WMGFTREGN SLFLPRNTPN IEPIMFNMYI INHNNSCIYF ENCYVSTVDF SLDKSIPILN VGIESGKFSE VSTFRDGYTI T QGEVLPYS ...String:
MFYSLMRESK IVIEYDGRGY HFDALSNYDA STSFQEFKTL RRTIHNRTNY ADSIINAQDP SSISLAINFS TTLIESNFFD WMGFTREGN SLFLPRNTPN IEPIMFNMYI INHNNSCIYF ENCYVSTVDF SLDKSIPILN VGIESGKFSE VSTFRDGYTI T QGEVLPYS APAVYTNSSP LPALISASMS FQQQCSWRED RNIFDINKIY TNKRAYVNEM NASATLAFYY VKRLVGDKFL NL DPETRTP LIIKNKYVSI TFPLARISKR LNFSDLYQVE YDVIPTADSD PVEINFFGER K

UniProtKB: Baseplate tube protein p140

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Macromolecule #2: Distal tail protein pb9

MacromoleculeName: Distal tail protein pb9 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 22.798641 KDa
SequenceString: MRLPDPYTNP EYPGLGFESV NLVDNDPMIR DELPNGKVKE VKISAQYWGI NISYPELFPD EYAFLDSRLL EYKRTGDYLD VLLPQYEAF RVRGDTKSVT IPAGQKGSQI ILNTNGTLTG QPKAGDLFKL STHPKVYKIT NFSSSGNVWN ISLYPDLFIT T TGSEKPVF ...String:
MRLPDPYTNP EYPGLGFESV NLVDNDPMIR DELPNGKVKE VKISAQYWGI NISYPELFPD EYAFLDSRLL EYKRTGDYLD VLLPQYEAF RVRGDTKSVT IPAGQKGSQI ILNTNGTLTG QPKAGDLFKL STHPKVYKIT NFSSSGNVWN ISLYPDLFIT T TGSEKPVF NGILFRTKLM NGDSFGSTLN NNGTYSGISL SLRESL

UniProtKB: Distal tail protein pb9

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Macromolecule #3: Baseplate hub protein pb3

MacromoleculeName: Baseplate hub protein pb3 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 107.279766 KDa
SequenceString: 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

UniProtKB: Baseplate hub protein pb3

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30589
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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