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Open data
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Basic information
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Title | Connector complex of bacteriophage JBD30 computed in C12 symmetry | |||||||||
![]() | main_map | |||||||||
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![]() | bacteriophage JBD30 / virion / connector complex / portal protein / adaptor protein / VIRUS | |||||||||
Function / homology | Protein of unknown function DUF935 / Protein of unknown function (DUF935) / Bacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / Portal protein / DUF1320 domain-containing protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
![]() | Valentova L / Fuzik T / Plevka P | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 21.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.3 KB 20.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 118.9 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 405.1 MB 405.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rkbMC ![]() 19256 ![]() 19257 ![]() 19258 ![]() 19259 ![]() 19260 ![]() 19261 ![]() 19262 ![]() 19263 ![]() 19264 ![]() 19265 ![]() 19266 ![]() 19268 ![]() 19269 ![]() 19270 ![]() 19271 ![]() 19272 ![]() 19273 ![]() 19274 ![]() 19280 ![]() 19281 ![]() 19285 ![]() 19439 ![]() 19561 ![]() 8rk3C ![]() 8rk4C ![]() 8rk5C ![]() 8rk6C ![]() 8rk7C ![]() 8rk8C ![]() 8rk9C ![]() 8rkaC ![]() 8rkcC ![]() 8rknC ![]() 8rkoC ![]() 8rkxC ![]() 8rqeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Pseudomonas phage JBD30
Entire | Name: ![]() |
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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 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: ![]() ![]() |
Molecular weight | Theoretical: 874 KDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 57.791332 KDa |
Sequence | String: MAQIVDVYGN PIRTQQLREP QTSRLAGLAK EFAQHPAKGL TPAKLARILV EAEQGNLQAQ AELFMDMEER DAHLFAEMSK RKRAILGLD WAVEPPRNAS AAEKADADYL HELLLDLEGL EDLLLDALDG IGHGYSCIEL EWALQGREWM PLAFHHRPQS W FQLNPEDQ ...String: MAQIVDVYGN PIRTQQLREP QTSRLAGLAK EFAQHPAKGL TPAKLARILV EAEQGNLQAQ AELFMDMEER DAHLFAEMSK RKRAILGLD WAVEPPRNAS AAEKADADYL HELLLDLEGL EDLLLDALDG IGHGYSCIEL EWALQGREWM PLAFHHRPQS W FQLNPEDQ NELRLRDNSP AGEALQPFGW IIHRPRARSG YVARSGLFRV LAWPYLFRHY ATSDLAEMLE IYGLPIRLGK YP PGTADEE KATLLRAVTG LGHAAAGIIP ETMAIDFQQA AQGSSDPFLA MMRQSEDAIS KAVLGGTLTS TTSQSGGGAF ALG QVHNEV RHDLLASDAR QLAATLSRDL LWPLLVLNRP GSPDVRRAPR LVFDLREQAD ITSMAQSIPA LVNVGLEIPS AWVY DKLGI PQPAKNEPVL RSAAQPAILS RQHGQRVAAL ATIVGPRYGD QQALDKALAS LPAKDMQDQV NDLLAPLLEA VNRGD SETE LLGALAEAFP DMDDSALTDA LHRLLFAADT WGRLHGNLDR ID UniProtKB: Portal protein |
-Macromolecule #2: DUF1320 domain-containing protein
Macromolecule | Name: DUF1320 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.155176 KDa |
Sequence | String: MSYCTLADLI EQYSEQKIRE VSDRVNKPAT TIDTVIVDRA IADADSEIDL HLHGRYQLPL ASVPTALKRI ACGLAYANLH IVLKEENPV YKTAEHLRKL LSGIANGKLS LALDADGKPA PVANTVQISE GRNDWGADW UniProtKB: DUF1320 domain-containing protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
Details: 10 mM MgSO4, 10 mM NaCl, 50 mM Tris pH 8 | ||||||||||||
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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 2 s, waiting time 15 s. | ||||||||||||
Details | phage titer 10^11 PFU |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8rkb: |