+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19256 | |||||||||
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Title | Bacteriophage JBD30 baseplate - composite structure | |||||||||
Map data | composite map of bacteriophage jbd30 baseplate | |||||||||
Sample |
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Keywords | bacteriophage JBD30 / virion / baseplate / VIRUS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas phage JBD30 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.46 Å | |||||||||
Authors | Valentova L / Fuzik T / Plevka P | |||||||||
Funding support | Czech Republic, European Union, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19256.map.gz | 32.9 MB | EMDB map data format | |
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Header (meta data) | emd-19256-v30.xml emd-19256.xml | 27.3 KB 27.3 KB | Display Display | EMDB header |
Images | emd_19256.png | 150.6 KB | ||
Filedesc metadata | emd-19256.cif.gz | 8.8 KB | ||
Others | emd_19256_additional_1.map.gz | 54.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19256 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19256 | HTTPS FTP |
-Related structure data
Related structure data | 8rk3MC 19257 19258 19259 19260 19261 19262 19263 19264 19265 19266 19267 19268 19269 19270 19271 19272 19273 19274 19280 19281 19285 19439 19561 8rk4C 8rk5C 8rk6C 8rk7C 8rk8C 8rk9C 8rkaC 8rkbC 8rkcC 8rknC 8rkoC 8rkxC 8rqeC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19256.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | composite map of bacteriophage jbd30 baseplate | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8336 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Pseudomonas phage JBD30
Entire | Name: Pseudomonas phage JBD30 (virus) |
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Components |
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-Supramolecule #1: Pseudomonas phage JBD30
Supramolecule | Name: 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 |
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Host (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: BAA-28 |
Molecular weight | Theoretical: 1.713 MDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Tape measure protein N-terminal domain-containing protein
Macromolecule | Name: Tape measure protein N-terminal domain-containing protein type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 120.920586 KDa |
Sequence | String: 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 |
-Macromolecule #2: DUF2163 domain-containing protein
Macromolecule | Name: DUF2163 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 29.979053 KDa |
Sequence | String: 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 |
-Macromolecule #3: Virion structural protein
Macromolecule | Name: Virion structural protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 62.163148 KDa |
Sequence | String: 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 |
-Macromolecule #4: DUF2793 domain-containing protein
Macromolecule | Name: DUF2793 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 40.578426 KDa |
Sequence | String: 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 |
-Macromolecule #5: Tip attachment protein J domain-containing protein
Macromolecule | Name: Tip attachment protein J domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 79.898781 KDa |
Sequence | String: 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 |
-Macromolecule #6: Virion structural protein
Macromolecule | Name: Virion structural protein / type: protein_or_peptide / ID: 6 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 35.014137 KDa |
Sequence | String: 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 |
-Macromolecule #7: Virion structural protein
Macromolecule | Name: Virion structural protein / type: protein_or_peptide / ID: 7 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 33.358809 KDa |
Sequence | String: 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 |
-Macromolecule #8: Virion structural protein
Macromolecule | Name: Virion structural protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 26.983729 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 10 mM NaCl, 10 mM MgSO4, 50 mM Tris-HCl | ||||||||||||
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solaris II | ||||||||||||
Vitrification | Cryogen 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. | ||||||||||||
Details | phage titer 10^11 PFU/ml |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8rk3: |