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Open data
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Basic information
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Title | Scaffold rings inside the Borrelia bacteriophage BB1 procapsid | ||||||||||||
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Function / homology | Protein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Rumnieks J / Fuzik T / Tars K | ||||||||||||
Funding support | European Union, 3 items
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![]() | ![]() Title: Structure of the Borrelia Bacteriophage φBB1 Procapsid. Authors: Jānis Rūmnieks / Tibor Füzik / Kaspars Tārs / ![]() ![]() Abstract: Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all ...Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 34.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.2 KB | Display | ![]() |
Images | ![]() | 134.1 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 404 MB 404.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8phtMC ![]() 8phoC ![]() 8phpC ![]() 8phqC ![]() 8phrC ![]() 8phsC ![]() 8phuC ![]() 8pkhC ![]() 8qo0C ![]() 8qo1C 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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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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-Half map: #1
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-Half map: #2
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Density Histograms |
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Sample components
-Entire : Scaffold of the Borrelia bacteriophage BB1 procapsid
Entire | Name: Scaffold of the Borrelia bacteriophage BB1 procapsid |
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Components |
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-Supramolecule #1: Scaffold of the Borrelia bacteriophage BB1 procapsid
Supramolecule | Name: Scaffold of the Borrelia bacteriophage BB1 procapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Scaffold protein
Macromolecule | Name: Scaffold protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.710363 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MTEKEEKEDL QAQDKEEQQI KADTKVISVQ EFEEYMRFKE QANSKSKETS RDLSINERIT KELAEVEERE RIEKQLLLEA ERINEIDTL AKAHLSNHFN KEVLLAKGYT LKDIMQAQRR ELVRKFVPIE QIKAIAKVSD ISHIDGEILE QLVSLAKVNI K LRKNASSS ...String: MTEKEEKEDL QAQDKEEQQI KADTKVISVQ EFEEYMRFKE QANSKSKETS RDLSINERIT KELAEVEERE RIEKQLLLEA ERINEIDTL AKAHLSNHFN KEVLLAKGYT LKDIMQAQRR ELVRKFVPIE QIKAIAKVSD ISHIDGEILE QLVSLAKVNI K LRKNASSS SSSVDSIKGN IAIKSEERAS LLDSNFVPIN FTEFVQAISN TYKQRRIQFY ENLKRHKRTS IA UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Output model | ![]() PDB-8pht: |