+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19263 | |||||||||
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Title | Baseplate of bacteriophage JBD30 computed in C3 symmetry | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | bacteriophage JBD30 / virion / baseplate / distal tail protein / baseplate hub / baseplate upper protein / VIRUS | |||||||||
Function / homology | Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Uncharacterized protein / Virion structural protein 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_19263.map.gz | 54.8 MB | EMDB map data format | |
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Header (meta data) | emd-19263-v30.xml emd-19263.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19263_fsc.xml | 19.2 KB | Display | FSC data file |
Images | emd_19263.png | 143.7 KB | ||
Masks | emd_19263_msk_1.map | 600.7 MB | Mask map | |
Filedesc metadata | emd-19263.cif.gz | 7.2 KB | ||
Others | emd_19263_half_map_1.map.gz emd_19263_half_map_2.map.gz | 486.6 MB 486.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19263 | HTTPS FTP |
-Validation report
Summary document | emd_19263_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_19263_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_19263_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | emd_19263_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19263 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19263 | HTTPS FTP |
-Related structure data
Related structure data | 8rk7MC 8rk3C 8rk4C 8rk5C 8rk6C 8rk8C 8rk9C 8rkaC 8rkbC 8rkcC 8rknC 8rkoC 8rkxC 8rqeC M: atomic model generated by this map C: citing same article (ref.) |
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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_19263.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
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
-Mask #1
File | emd_19263_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_19263_half_map_1.map | ||||||||||||
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Annotation | half_map_2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_19263_half_map_2.map | ||||||||||||
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Annotation | half_map_1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: #1-#3 Details: Phage JBD30 was propagated in P. aeruginosa strain BAA-28 and purified using CsCl gradient. 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: 516 KDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: DUF2163 domain-containing protein
Macromolecule | Name: DUF2163 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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 #2: Virion structural protein
Macromolecule | Name: Virion structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: Tip attachment protein J domain-containing protein
Macromolecule | Name: Tip attachment protein J domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-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 Solarus II | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: blotting force 0, blotting time 2s, waiting time 15s. | ||||||||||||
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-8rk7: |