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- EMDB-60197: Portal-tail of Vibrio cholerae typing phage mature VP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60197
TitlePortal-tail of Vibrio cholerae typing phage mature VP1
Map data
Sample
  • Virus: Vibrio cholerae phage (bacteria)
    • Protein or peptide: nozzle gp16
    • Protein or peptide: portal gp5
    • Protein or peptide: adaptor gp12
    • Protein or peptide: ring protein gp10
    • Protein or peptide: gp13
Keywordsphage / virus / vibrio cholera phage / VIRAL PROTEIN
Biological speciesVibrio cholerae (bacteria) / Vibrio cholerae phage (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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: to be published
Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states
Authors: Liu HR / Pang H
History
DepositionMay 16, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_60197.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-7.103951 - 15.619445000000001
Average (Standard dev.)0.005217925 (±0.83986515)
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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Sample components

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Entire : Vibrio cholerae phage

EntireName: Vibrio cholerae phage (bacteria)
Components
  • Virus: Vibrio cholerae phage (bacteria)
    • Protein or peptide: nozzle gp16
    • Protein or peptide: portal gp5
    • Protein or peptide: adaptor gp12
    • Protein or peptide: ring protein gp10
    • Protein or peptide: gp13

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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: No

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Macromolecule #1: nozzle gp16

MacromoleculeName: nozzle gp16 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 59.015762 KDa
SequenceString: MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA GSGRRWNAVN FNGVLLMNNE LDSPQYLAAS GKLEDFPNLP SNVRFRTVAV YKNFILGLGV N FGSGFLDD ...String:
MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA GSGRRWNAVN 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 FAGEMWS

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Macromolecule #2: portal gp5

MacromoleculeName: portal gp5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 73.263602 KDa
SequenceString: MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEEEEEII ...String:
MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEEEEEII DGVPTGNMKK VKKTRVVKGY EGCKTFNVMV YDFIPDPRVA LCKYQEGEFF GRRLDLNVLD LKKGAKFGKY FN VEHAEAL VAASKEEMYR RDPSIGQQRS LKDSTMTPKG KQVGDISCVE IFVRLVPKDW GLGDSEFPEM WVFTVADKKY IVA AEPVNT LDDKFPFHIL ECEIDGYMNK SRGLLEISAP MNDILTWLFD SHMYNKRQIM NNQFIGDPSA LVVKDVESKE PGKF IRLRP TAYGRDVRSI ISQLPVTDVT AQNIQDVQVV ERNMQRIVGV NDDVAGQSSP SSRRSATEFR GTTSFASSRL ANLAY FFSV TGFRSLAKSL IVKTQQLYTV EMKVKVAGDN IKGAQSIIVK PEDISGQFDI MPVDGTLPVD RMAQAQFWMQ IMSMVA GNP VLGAEYRLGD IFSYTARLAG LKGIDKMKIR ILDDDQILAL ILAQQKGGAD VQPTGQPTTQ GVGNPTGVNE PAPSVTQ GT PGLSGLQALM

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Macromolecule #3: adaptor gp12

MacromoleculeName: adaptor gp12 / type: protein_or_peptide / ID: 3 / 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 #4: ring protein gp10

MacromoleculeName: ring protein gp10 / type: protein_or_peptide / ID: 4 / 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 #5: gp13

MacromoleculeName: gp13 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 10.025203 KDa
SequenceString:
MALETWDANS TPATLNTAWP EATDPLNKGD DHIRLLKTVV VNFWNKVFDG SKLKTAVVPA AVNSATAGSG FGGFRYQVVN NSDGTKTLR LFTS

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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47456
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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