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- EMDB-60199: portal-tail of Vibrio cholerae typing phage release VP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60199
Titleportal-tail of Vibrio cholerae typing phage release VP1
Map data
Sample
  • Virus: Vibrio cholerae phage (bacteria)
    • Protein or peptide: ring protein of release VP1
    • Protein or peptide: adaptor of release VP1
    • Protein or peptide: nozzle of release VP1
    • Protein or peptide: portal of release VP1
Keywordsphage / virus / vibrio cholera phage / VIRAL PROTEIN
Biological speciesVibrio cholerae (bacteria) / Vibrio cholerae phage (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsLiu HR / Pang H
Funding support China, 3 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)32200994 China
CitationJournal: Structure / Year: 2024
Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states.
Authors: Hao Pang / Fenxia Fan / Jing Zheng / Hao Xiao / Zhixue Tan / Jingdong Song / Biao Kan / Hongrong Liu /
Abstract: Lytic podophages (VP1-VP5) play crucial roles in subtyping Vibrio cholerae O1 biotype El Tor. However, until now no structures of these phages have been available, which hindered our understanding of ...Lytic podophages (VP1-VP5) play crucial roles in subtyping Vibrio cholerae O1 biotype El Tor. However, until now no structures of these phages have been available, which hindered our understanding of the molecular mechanisms of infection and DNA release. Here, we determined the cryoelectron microscopy (cryo-EM) structures of mature and DNA-ejected VP1 structures at near-atomic and subnanometer resolutions, respectively. The VP1 head is composed of 415 copies of the major capsid protein gp7 and 11 turret-shaped spikes. The VP1 tail consists of an adapter, a nozzle, a slender ring, and a tail needle, and is flanked by three extended fibers I and six trimeric fibers II. Conformational changes of fiber II in DNA-ejected VP1 may cause the release of the tail needle and core proteins, forming an elongated tail channel. Our structures provide insights into the molecular mechanisms of infection and DNA release for podophages with a tail needle.
History
DepositionMay 16, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60199.png

Downloads & links

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Map

FileDownload / File: emd_60199.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-4.463806 - 8.025615999999999
Average (Standard dev.)0.0031640257 (±0.52650577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60199_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_60199_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholerae phage

EntireName: Vibrio cholerae phage (bacteria)
Components
  • Virus: Vibrio cholerae phage (bacteria)
    • Protein or peptide: ring protein of release VP1
    • Protein or peptide: adaptor of release VP1
    • Protein or peptide: nozzle of release VP1
    • Protein or peptide: portal of release VP1

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Supramolecule #1: Vibrio cholerae phage

SupramoleculeName: Vibrio cholerae phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 666 / Sci species name: Vibrio cholerae phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: ring protein of release VP1

MacromoleculeName: ring protein of release VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 26.311119 KDa
SequenceString: MSSWDRFDTP WDSIIDESTW EHYTFKYDAS FEAFSSMEVD EDLTITVSVL FASTSDNTVT VGQVLGLTMD NRAGSYFGAG SSWTSEAAV NNEAGSGFQS SHALQLSYSV EDGVISSFGS EAFCSFYNTV SFESSSDVQA AVNSLYNLDV LFSSGSGDSE Q HYVVFGET ...String:
MSSWDRFDTP WDSIIDESTW EHYTFKYDAS FEAFSSMEVD EDLTITVSVL FASTSDNTVT VGQVLGLTMD NRAGSYFGAG SSWTSEAAV NNEAGSGFQS SHALQLSYSV EDGVISSFGS EAFCSFYNTV SFESSSDVQA AVNSLYNLDV LFSSGSGDSE Q HYVVFGET ASFESLAEHE TSSQYITHVE CMFNSVVEFE VKTYDWGRPV KPVGSDWSTD TPVVGVWVNE IYNGNKDWGE S

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Macromolecule #2: adaptor of release VP1

MacromoleculeName: adaptor of release VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 23.59285 KDa
SequenceString: MDKATLVKTI AYRMGNVKGQ DTAIDFELAL SIERLEGQEF VPWFLLSENN FFEGTAQENR IPVPRGFIRE YEEGSLYLRR VAGTGKCLI KKSQDQLLKY EGMTGEPSHY SLTNQYFRIY PVPQEDFKVE LLFYRKSSTL NVEDNPWYEY AAELLVAETI W AMLSARRD ...String:
MDKATLVKTI AYRMGNVKGQ DTAIDFELAL SIERLEGQEF VPWFLLSENN FFEGTAQENR IPVPRGFIRE YEEGSLYLRR VAGTGKCLI KKSQDQLLKY EGMTGEPSHY SLTNQYFRIY PVPQEDFKVE LLFYRKSSTL NVEDNPWYEY AAELLVAETI W AMLSARRD KMADYWKSVA ADQMRRLTIL DAERRLANQE IFMG

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Macromolecule #3: nozzle of release VP1

MacromoleculeName: nozzle of release VP1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 58.925699 KDa
SequenceString: MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA AAAARWNAVN FNGVLLMNNE LDSPQYLAAS GKLEDFPNLP SNVRFRTVAV YKNFILGLGV N FGSGFLDD ...String:
MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA AAAARWNAVN FNGVLLMNNE LDSPQYLAAS GKLEDFPNLP SNVRFRTVAV YKNFILGLGV N FGSGFLDD EIYWSHQADP GTMPPNWDYA NAASDSGRTP LPSEGYCVTS EELGSMNIVY KSDSIWTMQL IGGQWIFRFE NK FPGQGIL NKKSVVSFEG KHFVVTQKDI IVHDGYQVRS VADKRVRNFF FTDMNSDYFE RVFVVKDPRV AEVYVFYPSK NSV DGLCDR ALVWNWRDDV WSLLNLRPLK HAAYGYEITG VSITWDNFVG GWESTGLWQA DEDVAKYAPV LHYSFRDVPK LLAP TPQAL FIDEEIEAVW EREDIVIGSI SRDGVPYQDY ERNKSVSSIS FDVDTTEPFD VYIGYKGSLE DSVEWEFAGT VNPME DKRL FCLLTAGLFS MRIISKAQTF ILRSYKITYE FAGEMWA

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Macromolecule #4: portal of release VP1

MacromoleculeName: portal of release VP1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 66.026672 KDa
SequenceString: MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEVKKTRV ...String:
MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEVKKTRV VKGYEGCKTF NVMVYDFIPD PRVALCKYQE GEFFGRRLDL NVLDLKKGAK FGKYFNVEHA EALVAASKEE MY RRDPSIG QQRSLKDSTM TPKGKQVGDI SCVEIFVRLV PKDWGLGDSE FPEMWVFTVA DKKYIVAAEP VNTLDDKFPF HIL ECEIDG YMNKSRGLLE ISAPMNDILT WLFDSHMYNK RQIMNNQFIG DPSALVVKDV ESKEPGKFIR LRPIISQLPV TDVT AQNIQ DVQVVERNMQ RIVGVNDDVA GQSSPSSRRS ATEFRGTTSF ASSRLANLAY FFSVTGFRSL AKSLIVKTQQ LYTVE MKVK VAGDNIKGAQ SIIVKPEDIS GQFDIMPVDG TLPVDRMAQA QFWMQIMSMV AGNPVLGAEY RLGDIFSYTA RLAGLK GID KMKIRILDDD QILALILA

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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

Particle selectionNumber selected: 1698
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1698
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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