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- EMDB-36463: Portal-tail complex of phage GP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-36463
TitlePortal-tail complex of phage GP4
Map dataportal tail complex of phage GP4
Sample
  • Virus: Ralstonia phage GP4 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Putative tail fiber protein
    • Protein or peptide: Virion associated protein
    • Protein or peptide: Virion-associated phage protein
    • Protein or peptide: gp81 of phage GP4
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


Protein of unknown function DUF6682 / Family of unknown function (DUF6682) / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile.
Similarity search - Domain/homology
Portal protein / Virion-associated phage protein / Putative tail fiber protein / Uncharacterized protein / Virion associated protein
Similarity search - Component
Biological speciesRalstonia phage GP4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu H / Chen W
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Science Foundation (NSF, China)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: J Mol Biol / Year: 2023
Title: Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers.
Authors: Jing Zheng / Wenyuan Chen / Hao Xiao / Fan Yang / Jingdong Song / Lingpeng Cheng / Hongrong Liu /
Abstract: Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two ...Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments.
History
DepositionJun 8, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36463.png

Downloads & links

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Map

FileDownload / File: emd_36463.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationportal tail complex of phage GP4
Voxel sizeX=Y=Z: 1.27 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-13.8104105 - 31.900856000000001
Average (Standard dev.)-0.00037615976 (±1.6495419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 508.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1

Fileemd_36463_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_36463_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ralstonia phage GP4

EntireName: Ralstonia phage GP4 (virus)
Components
  • Virus: Ralstonia phage GP4 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Putative tail fiber protein
    • Protein or peptide: Virion associated protein
    • Protein or peptide: Virion-associated phage protein
    • Protein or peptide: gp81 of phage GP4

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Supramolecule #1: Ralstonia phage GP4

SupramoleculeName: Ralstonia phage GP4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2282904 / Sci species name: Ralstonia phage GP4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 87.929188 KDa
SequenceString: MFDLRDDQNT RVIADHPEAR MPTEEPGKDD APPSHPLDSE EMKELHRRLR SYLHQELDRQ AENRFQMAVD EDYYDSIQWT EADAQVLKE RGQAPLVFNV IAQSVNWIIG SEKRGRTDFN ILPRKKADAK PAEAKTKLLK YLSDVNRLPF HRSRSFEDTV K VGLGWIED ...String:
MFDLRDDQNT RVIADHPEAR MPTEEPGKDD APPSHPLDSE EMKELHRRLR SYLHQELDRQ AENRFQMAVD EDYYDSIQWT EADAQVLKE RGQAPLVFNV IAQSVNWIIG SEKRGRTDFN ILPRKKADAK PAEAKTKLLK YLSDVNRLPF HRSRSFEDTV K VGLGWIED SYDDSTDGEP IYSRYESWRN VIFDSASTEL DGTDMRYIFR PKWLDVDVAC ALVPDRADEI KKAAVAAERY GN YSEEDGD EAMDWAEFDR DTYSQSRTVS THKRQRVRLI ECWYRKPMRA TKFLSGDLRG ETLDESNPAH VEARDSGLYS LGE RITMRV RVAIFTSRDL LFEGASPFRH NRFSLTPIWG FRRGRDNLPY GVIRWMRDIQ DDINKRASKA LYILSSNKVV MDEG AVEDI EEFREEVARP DAVLVKKPGK QIELNVDREL AAAHMDMMSR DIQMLQQVGG VTDELMGRST NAVSGVAIQA RQEQG TVAT NKLFDNLRFA VQMQGEIQLS LIEQFVTEEK TFRITNERGK ADFITVNDGL PENDIVRTKA DFIIGESDWR ATYRQA ASE QLSQMIMKMP PQVGLVMLDL WADSTDLPNR DEIVKRIRQI NGMRDPDATE PTPEELQQQQ AAAEQAQAQK AMFMAEL SE KQGKADKAQA DAVAAQANAD LRAAQAEQVR RQTVNTNVTS IAAAMEAATA IVTMPTIAKV GDAVLVEAGY ENNGIAPA G GLHTPAPQQA VNPAAQGLPP QQPQPQQPQE PAVSPSPEQL NGAAPSNTGE PVTPDQTLQQ

UniProtKB: Portal protein

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Macromolecule #2: Putative tail fiber protein

MacromoleculeName: Putative tail fiber protein / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 45.894781 KDa
SequenceString: MAAVQFANNA ASRLVGPLAP SGTSLTVTPG DGALFPTLGA GDWFMATLIR SDGAREIVKV TSRTVDAMSI TRAQEGSSAL SFNPNDRIE ARLTAGELGD FRDGIASAQS AASAAQGTAD GKISKAGDTM TGNLNMEGAA PIITFRETDQ AAPAGRWRLV A DGGNWSLR ...String:
MAAVQFANNA ASRLVGPLAP SGTSLTVTPG DGALFPTLGA GDWFMATLIR SDGAREIVKV TSRTVDAMSI TRAQEGSSAL SFNPNDRIE ARLTAGELGD FRDGIASAQS AASAAQGTAD GKISKAGDTM TGNLNMEGAA PIITFRETDQ AAPAGRWRLV A DGGNWSLR RSTAGEFASE NSTMWFGPDD SVHFLNDILI GRGNLGSVYD ALASKATSAA LASGLSAKPD ADGVSVTGFV NG NFYEPYF RKSSDNTVRR LVANTSANGI ALSWSGSFLS RTIDNTATAT IWDTANAPGA GTTNLDKTFY CGDGTRIGRS WVP GSGFLS ITVDGTNYGI SISASDERLK REIAPSEASA LSKLGRIELF SFRYKEGNAF LDPSQHHDIG FIAQQLASVD PTFV AGGGE TMLSPNLQPI VATLVKAVQE LRSQVDALKA QVGA

UniProtKB: Putative tail fiber protein

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Macromolecule #3: Virion associated protein

MacromoleculeName: Virion associated protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 23.545262 KDa
SequenceString: MAFPASVVLS RAATLLQDED HERWTVDELL EWLTDGTREI VVRKPSAYMK TTTAALVAGS KQALPEDAIQ LIDVPRNLKT DGSPGRAVT ATDRRLLDTE NPDWHSMKPA GQIRHYTYDS NVPTVFYTYP PAAAGVQVEL VCAWRHPALT TQNDVVQMGA E FVSALVSW ...String:
MAFPASVVLS RAATLLQDED HERWTVDELL EWLTDGTREI VVRKPSAYMK TTTAALVAGS KQALPEDAIQ LIDVPRNLKT DGSPGRAVT ATDRRLLDTE NPDWHSMKPA GQIRHYTYDS NVPTVFYTYP PAAAGVQVEL VCAWRHPALT TQNDVVQMGA E FVSALVSW CLYRASSKDS EFANGAVAAA HYSAFSDALG AQATGTPTTQ AAAAAAAAGA AQ

UniProtKB: Virion associated protein

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Macromolecule #4: Virion-associated phage protein

MacromoleculeName: Virion-associated phage protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 62.764598 KDa
SequenceString: MTTLKLTAYS GEVPRTLPRL LPDTASQRAL NVRLDNGGLT PTRQPRFEAN ISVDNAKTIY KHNGAWLAWQ NVVHAAPGPV AQDRLYYMG DGKPKMIVDG TTYDLAVPMP TAAPALTVTG TGTGNVTSIA YVYTFVTAFG EESEPSALSN VAGWQSGQTR T LTGIQAPP ...String:
MTTLKLTAYS GEVPRTLPRL LPDTASQRAL NVRLDNGGLT PTRQPRFEAN ISVDNAKTIY KHNGAWLAWQ NVVHAAPGPV AQDRLYYMG DGKPKMIVDG TTYDLAVPMP TAAPALTVTG TGTGNVTSIA YVYTFVTAFG EESEPSALSN VAGWQSGQTR T LTGIQAPP AGRNITKQRF YRSQTGSGGT DLFFIEERAA SAANFVDTHA TNDFGEMLPS LEYNAPPDGL KGLISLPNGM MA AFTGKDL YFCEPFIPHA WPEKYILTMD YQIVALGAYG TTIVVMTEGL PYIVSGTAPE NMQQQRVELN LPCINARGVI DLG YSVAYP SHDGLVMAGS NGMQVITEQL MTRNDWMKTG PGNIVGGQFN GRYFASYEYI EPSGAAFSGT LIFDTTGAAP FIIR SNHKA DAFFHELQTG ALYFLVGKEI FEWDALGQVN ETLSWRSKQF VLPMPTNFGA ILIEGSTAAS EEEQAAYDAE RQRIE VENA TNFALPSIGG EMNGAEVNLF AVNGDMMQRL PAEGFVSVSI YADGKLVKTV SKMNRMARLP SGFLARIWEI EVNSNI NIS DIVLATTGQE LRNV

UniProtKB: Virion-associated phage protein

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Macromolecule #5: gp81 of phage GP4

MacromoleculeName: gp81 of phage GP4 / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 23.197357 KDa
SequenceString: MKPLDVFMPI IHRFAPGCPE PTAFAAIREA AIKFCERTRL WRCDDEFNVG ADECAEVAVP YGAALYEMEL VQFNGRNMRP VSTQWLDEQ VPDWRTTTQS GQAQYVTQQS EDTLTFVPAE AGSVRVYGLL KPTLDADSLP DLLADTYRKT IADGALSELL I IPGKAWMS ...String:
MKPLDVFMPI IHRFAPGCPE PTAFAAIREA AIKFCERTRL WRCDDEFNVG ADECAEVAVP YGAALYEMEL VQFNGRNMRP VSTQWLDEQ VPDWRTTTQS GQAQYVTQQS EDTLTFVPAE AGSVRVYGLL KPTLDADSLP DLLADTYRKT IADGALSELL I IPGKAWMS ADLAVFFGTR FDRELDRLST KTIKGQQRAP VRTRAQFF

UniProtKB: Uncharacterized protein

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39883
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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