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- EMDB-19256: Bacteriophage JBD30 baseplate - composite structure -

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Basic information

Entry
Database: EMDB / ID: EMD-19256
TitleBacteriophage JBD30 baseplate - composite structure
Map datacomposite map of bacteriophage jbd30 baseplate
Sample
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: Tape measure protein N-terminal domain-containing protein
    • Protein or peptide: DUF2163 domain-containing protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: DUF2793 domain-containing protein
    • Protein or peptide: Tip attachment protein J domain-containing protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Virion structural protein
Keywordsbacteriophage JBD30 / virion / baseplate / VIRUS
Function / homology
Function and homology information


Tape measure protein N-terminal / Tape measure protein / Protein of unknown function UCP028589 / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599
Similarity search - Domain/homology
Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Virion structural protein / Virion structural protein / Uncharacterized protein / Virion structural protein / Virion structural protein / DUF2793 domain-containing protein / Tape measure protein N-terminal domain-containing protein
Similarity search - Component
Biological speciesPseudomonas phage JBD30 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsValentova L / Fuzik T / Plevka P
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
European Research Council (ERC)101043452European Union
CitationJournal: Embo J. / Year: 2024
Title: Structure and replication of Pseudomonas aeruginosa phage JBD30
Authors: Valentova L / Plevka P / Fuzik T / Novacek J / Pospisil J
History
DepositionDec 23, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19256.png

Downloads & links

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Map

FileDownload / File: emd_19256.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of bacteriophage jbd30 baseplate
Voxel sizeX=Y=Z: 0.8336 Å
Density
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-16.154468999999999 - 36.303657999999999
Average (Standard dev.)0.060019944 (±1.0610468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 450.14398 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Pseudomonas phage JBD30

EntireName: Pseudomonas phage JBD30 (virus)
Components
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: Tape measure protein N-terminal domain-containing protein
    • Protein or peptide: DUF2163 domain-containing protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: DUF2793 domain-containing protein
    • Protein or peptide: Tip attachment protein J domain-containing protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Virion structural protein
    • Protein or peptide: Virion structural protein

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Supramolecule #1: Pseudomonas phage JBD30

SupramoleculeName: Pseudomonas phage JBD30 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1223260 / Sci species name: Pseudomonas phage JBD30 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: BAA-28
Molecular weightTheoretical: 1.713 MDa
Virus shellShell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: Tape measure protein N-terminal domain-containing protein

MacromoleculeName: Tape measure protein N-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 120.920586 KDa
SequenceString: MATNQQLSIA LRIQADLAEA QNALRQLTGN LQQVDRGAVQ TRSELSAMGG QLDSLRAQVL GFVGAWASLS ALGGLVTMVD QYGQMADRI QMVTSSTAEY EQVQARLLET ASRTYRPLAE AQELYIRTAD SLKSLRYTTE QALDITDSFS FLLVTNAASA D RAASAIDA ...String:
MATNQQLSIA LRIQADLAEA QNALRQLTGN LQQVDRGAVQ TRSELSAMGG QLDSLRAQVL GFVGAWASLS ALGGLVTMVD QYGQMADRI QMVTSSTAEY EQVQARLLET ASRTYRPLAE AQELYIRTAD SLKSLRYTTE QALDITDSFS FLLVTNAASA D RAASAIDA YSKSIQTGKV SSDAWQSIMA AMPSLVNALA ESTGKSTEEI RKLGIEGSLS LRDLNEGLRK TVAANREAAD NM GTSVQDA LVSLNNALSA YLGELNRTYD ITGSVSSALN VLAENMEVIV KLFGVAAVAG LTRYVASLTL ATQAKLAAVL AAR AQAAEE LRTAQAQVAS TAAAAANARA QAGLTVSHTQ AAAAEAAHTA ATQRLAAAQL AAGAAMRGML AVIGGPAGIA MLVA GAAAS FFLFRDSAQA VKSSLDDLSE PLDQVVERMG KLSEIEQDRE LTRLSEQIDG LRQTAVEAAR EMREVASTAL YGARL DRIP SAEAQQALQP LIDASADAAR GVEVDWKSVM DTLAASGAVP DSLKRKLLDM AAGQAEAGRT ATELGQRHAE LKARLE GST AAINENSDAL SKGSDKAAEY IQSLRLAIAD LEDPSVLGKA GRRLQQFGAD LNAEQSAEIL RLETLKANTE KAAQARE DA RRKAESSARQ QASTAEQLAK SQEGYVAGLE KQARTLGLTS AEVRAYELAE KGLTGALHAR AAAALAALAA DEKKRQAD A NARTNAGLEA EYLRATGRTV DAGLLEIRTK FDAMRRDFEK AGNDAGLAWI DKLIPVAEAK VRLDDVKQQM DDLLADQQR AESSVNVQQD AGVINEMDAR QRILDIHRAT YEKLQQIRPI LEQMARQPGE VGRAAAESLA QLDAEAARLQ QTTTLLETTL RDGLTTGFT DAIKGLASGT MDLRDAITSL GEAVLNALVN MAAQNLAQSL SSGIMGLFGG GQQDTSMTTG AAAVTASAGA L STAGASLL TGAAAIQAAA ASLAAANGVQ GLGAAAGGAG AAGAAAGGGS WLSSIAGIFG FASGGHIKGP GTGTSDSIPI LA SNDEFMT RAAVVRQPGA LAFLEQFNRY GMAALAGWAN PVRHATGGQI GTPAPNLPAP VRAGANLPEP SKNFSTSVAN SIY LHAVQD TDQMAADMWA GKGGEHFLVW LNKNRQAVKQ II

UniProtKB: Tape measure protein N-terminal domain-containing protein

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Macromolecule #2: DUF2163 domain-containing protein

MacromoleculeName: DUF2163 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 29.979053 KDa
SequenceString: MSFNSRESSL ADGQPVRLYQ FSRGAIRWSY NSSDRDITYQ NQIFRTVPGG ITDNGIICSG DPQSDQFVIT APADLDVALL YKTRSPSDA IDLVVYDMHY GDAEAAVSWV GQIGDVDWPT VDSCRITCVS EDELMDQPGL TDTYCRTCTA IVGDHRCKVN L VPYRVTLT ...String:
MSFNSRESSL ADGQPVRLYQ FSRGAIRWSY NSSDRDITYQ NQIFRTVPGG ITDNGIICSG DPQSDQFVIT APADLDVALL YKTRSPSDA IDLVVYDMHY GDAEAAVSWV GQIGDVDWPT VDSCRITCVS EDELMDQPGL TDTYCRTCTA IVGDHRCKVN L VPYRVTLT PQSVSAWVIS SGVVAGYADG WFTGGYVEWQ VDGDNYDRRF IEQHAGADLH ILGGTEGIPA GGQLRVYPGC DG LAQTCDD KFSNLPNFRG FNAMQGKSPF DGDQVW

UniProtKB: Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein

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Macromolecule #3: Virion structural protein

MacromoleculeName: Virion structural protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 62.163148 KDa
SequenceString: MATFPGFQVP KPVEGIVAGI TPNIDALELN QDISLAAVAA STWGGAYGAH QPVEVIHSTY QAVHQSALEE NYYNRLWLIP TAMELGNVV STQIRPASVW NAYFSPRTLT AIDREAADGI TLSGQASPPL GFAALEERTW TVSIGTDGPP VVNARIVWRL Q GEPNLVLV ...String:
MATFPGFQVP KPVEGIVAGI TPNIDALELN QDISLAAVAA STWGGAYGAH QPVEVIHSTY QAVHQSALEE NYYNRLWLIP TAMELGNVV STQIRPASVW NAYFSPRTLT AIDREAADGI TLSGQASPPL GFAALEERTW TVSIGTDGPP VVNARIVWRL Q GEPNLVLV ITGNRIIAWT FAPDWGDSIV ERLSASTNIL QSESAVTQRR AMRLAPRREF DANMYAVDRE RQLLDMTLFG WG ARIWALP IWPDIQLLHQ PLAAGSLGIP CDTAGLDFRD GGLAMLRGED AFTYEVVEVK TVTASGLDLV RPVQAAWGTG SRL YPVRTA QLTEQPTLTR LTDTAQSARV SFLVMEPSAW PELMPATTYR GRPVLEQRPD ESEDLTSSYQ RLLSTLDNGS AIPR VTDVA GMALPVIGHR WIGMGRAERS AFRSLVYALR GQQKPLWVPT HADDLTLVAT VSQLSTALDV RNIGYARFAN GRPGR RDIR IELYDGTVYH RRILTSTELD ADTERVAIDA ALGRLVEPTD VARICFMALC SAASDVVEIE HVTDSEGVAT AALTFK GVR DDEF

UniProtKB: Virion structural protein

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Macromolecule #4: DUF2793 domain-containing protein

MacromoleculeName: DUF2793 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 40.578426 KDa
SequenceString: MTLYMGPNTG LLINGLPGEG HYSDLIRMWR WDDFLRQPVV KGRVATLPTT GQAEGDTYIF TGSGSNQNRL ARWWATGATT AIWEYMPPR LGWRVQVANE TTPSGQVKTY EYSGTAWVEL VGGMSDAPSD GKAYARESGA WTELGSAAKS ALNVLPFMNL M PDMGRFAG ...String:
MTLYMGPNTG LLINGLPGEG HYSDLIRMWR WDDFLRQPVV KGRVATLPTT GQAEGDTYIF TGSGSNQNRL ARWWATGATT AIWEYMPPR LGWRVQVANE TTPSGQVKTY EYSGTAWVEL VGGMSDAPSD GKAYARESGA WTELGSAAKS ALNVLPFMNL M PDMGRFAG TAANPLATMF TTSWTPSSFL NGWNGATVAD GGKFAFDNST NGGAGPALNA RVQALLAAMG RTWTSVSRYG VE FFTAVLT AGSQTTTGSA GADGVTRYLC CSNGSKTVFN AGGWATVVMW LRVESGSAHI SSAPYTTHRL WINGAVAAPG VVL PANQWV HLRFSMQSYN GYDNACPYIY ASAGAQIAFA CPAWFGGLVD PGIHVAPILT INGASA

UniProtKB: DUF2793 domain-containing protein

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Macromolecule #5: Tip attachment protein J domain-containing protein

MacromoleculeName: Tip attachment protein J domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 79.898781 KDa
SequenceString: MGAKPKAQTV GWRYYFDIHF ALGKKVDEVC AIRASGKTAW KGSITSNGQV RINAPELFGG DKGEGGLDGT LDVLFGEEDQ GVLPRLAAM LGGLVPAFRG VTTCFYSGLV TSVNPYPKKW EILRRGGNRL WDGNPWYPEK QFVWLADGQI KAMNPAHILY L VYTGRDFR ...String:
MGAKPKAQTV GWRYYFDIHF ALGKKVDEVC AIRASGKTAW KGSITSNGQV RINAPELFGG DKGEGGLDGT LDVLFGEEDQ GVLPRLAAM LGGLVPAFRG VTTCFYSGLV TSVNPYPKKW EILRRGGNRL WDGNPWYPEK QFVWLADGQI KAMNPAHILY L VYTGRDFR GLARTRMDEA SWRAAADTLY AEGFGLCFEW TRSDSFKNFC ETVKSHIGAE VYPNRQTGQI SIRLLRDDYN VA DLPLFDE DSGLLEITQE KTGSTSLAPS QLIVKYIDQI DGAQRQIIVN NNAVAASQGR RSSEEIEFLG VPTGELAGRV GER EMRLKT TGLKRYKGVF DRRARSLNPG QPFLIRSTPR GIPETVVRVG RIEDNFLGDG KITLTVVQDQ FNLPATTGVA PPPP GWTPP DRTPRAITVR RLIEAPYREL AGVIDPANLQ LLDVSASYLA ALAEAPTSLS QSYTLTDRVG SSGAFVDRGT GDWCP TGLL AAELPLAAGP NVVTLTNATR LEDVTVGQAA VVDDEIVRVD AVNYASGTVT LARGCADTVP AKHLAGARVW FYDTFE AVD ETVYSQGVTL QARLLTNTSE GQLAPALAAT DSLTLTGRQG KPYPPGQFRI NGSAYPTKVY GALSVSWAKR DRIGQAD QL IDTTVGNIGP EDGATVTLQV YSGTTLKRTY AGLTSSSWSY PLAEDMADGP LQDVRLVLRS VRDGIDSWQQ HDITIERH G LGFRLGEELG GVSA

UniProtKB: Uncharacterized protein

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Macromolecule #6: Virion structural protein

MacromoleculeName: Virion structural protein / type: protein_or_peptide / ID: 6 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 35.014137 KDa
SequenceString: MATEFGTAVN HADLVERLVQ FLTASPDLVA AGQAYEKVFD NTIPASGTAI AVRQVTLRAP GLGGTDAIYM GIQSYGDTAL DYYNLRLMG GTAFNPGAIP PGGDYWTAFA NYSPRVQLLA WNQPMPYWFF ANGRRFWIVV KVSTIYESAG AGFILPPCPP S QYPYPLAV ...String:
MATEFGTAVN HADLVERLVQ FLTASPDLVA AGQAYEKVFD NTIPASGTAI AVRQVTLRAP GLGGTDAIYM GIQSYGDTAL DYYNLRLMG GTAFNPGAIP PGGDYWTAFA NYSPRVQLLA WNQPMPYWFF ANGRRFWIVV KVSTIYESAG AGFILPPCPP S QYPYPLAV VGSYRGDVAT RWSDVSDRHR GISSPYERSC YLRDPAGRWL GFTVDGGAAN ESDYNNRTLL PLGCGRYAGS SD TVVKQLR DSFGKFPLKA LQFVTRETEG RRYLGDFDGA FYVPTLNSGA EDVIVEDGVD HVVFQTAWRS GNPWLYAIRK D

UniProtKB: Virion structural protein

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Macromolecule #7: Virion structural protein

MacromoleculeName: Virion structural protein / type: protein_or_peptide / ID: 7 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 33.358809 KDa
SequenceString: MAYFTGTANN PADLLAKVRV HAESLGWVTD RASASEWLCH NADGYWSFNA GANQFQMAGN TGFDNSLAWN AQPGNSVQNN PYSSKGPTV AQLSGGPFTR YHLFATAAYL HLHVEIAAGQ FRPVMIGSLN KRGVGYTGGQ YVCGSFIYTP GQALTNNWSS H PFDGYHIQ ...String:
MAYFTGTANN PADLLAKVRV HAESLGWVTD RASASEWLCH NADGYWSFNA GANQFQMAGN TGFDNSLAWN AQPGNSVQNN PYSSKGPTV AQLSGGPFTR YHLFATAAYL HLHVEIAAGQ FRPVMIGSLN KRGVGYTGGQ YVCGSFIYTP GQALTNNWSS H PFDGYHIQ YSNSSCMLRL DGLDGGPSPE WLPFDYTTNV PRRVVGPGRG NYSSQYHPDV GLIDASANEL NSSTTTVPCA IY AFGAQQR SRYVGEVPDF GICNMAFLAP GDPLVVGSDT WRVYPLLQRG TATDFDSTSA WVGYCFRVVE

UniProtKB: Virion structural protein

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Macromolecule #8: Virion structural protein

MacromoleculeName: Virion structural protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 26.983729 KDa
SequenceString: MAQETYFYGQ GEIDAAPIVN GVLGKWRWIQ DVSAMSIQLA VEKVEHKESY SGQKALVRSF PIGKTATVNI TLHSIGPDNL ALTLYGKVV AKAAGSVTGE VLPADLVAGD VIRLANFGVS ELVITDSASS PAPLDPQYYA LRADGAYGEV QLLGLPTPAP T QPFKAAYE ...String:
MAQETYFYGQ GEIDAAPIVN GVLGKWRWIQ DVSAMSIQLA VEKVEHKESY SGQKALVRSF PIGKTATVNI TLHSIGPDNL ALTLYGKVV AKAAGSVTGE VLPADLVAGD VIRLANFGVS ELVITDSASS PAPLDPQYYA LRADGAYGEV QLLGLPTPAP T QPFKAAYE YAATKQVGMF TAPQPTVALR YKGINLAEGG APVIVELYKV ATDPLQELAL ISDGNTVAGM QISGGILLDT SK PDTGDLG RFGRIIQLG

UniProtKB: Virion structural 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: 8
Component:
ConcentrationFormulaName
10.0 mMNaClsodium chloride
10.0 mMMgSO4magnesium sulphate
50.0 mMTris-HCltris hydrochloride

Details: 10 mM NaCl, 10 mM MgSO4, 50 mM Tris-HCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solaris II
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: blotting time 2, blotting force 0, waiting time 5.
Detailsphage titer 10^11 PFU/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12356 / Average exposure time: 2.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8376
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 1780
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8rk3:
Bacteriophage JBD30 baseplate - composite structure

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