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- PDB-8phu: Asymmetric structure of the portal-containing cap of the Borrelia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8phu | ||||||||||||
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Title | Asymmetric structure of the portal-containing cap of the Borrelia bacteriophage BB1 procapsid | ||||||||||||
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![]() | VIRAL PROTEIN / Portal / capsid / procapsid / scaffold | ||||||||||||
Function / homology | Uncharacterised conserved protein UCP020357 / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like / Protein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein / Phage portal protein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.41 Å | ||||||||||||
![]() | Rumnieks, J. / Fuzik, T. / Tars, K. | ||||||||||||
Funding support | European Union, 3items
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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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 13.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.7 MB | Display | ![]() |
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Full document | ![]() | 7.3 MB | Display | |
Data in XML | ![]() | 1.8 MB | Display | |
Data in CIF | ![]() | 2.6 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17675MC ![]() 8phoC ![]() 8phpC ![]() 8phqC ![]() 8phrC ![]() 8phsC ![]() 8phtC ![]() 8pkhC ![]() 8qo0C ![]() 8qo1C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 395 molecules ABACAJAKALASATAUBBBCBDBKBLBMBTBUBVCCCDCECLCMCNCUCVCWDBDCDJDK...
#1: Protein | Mass: 36255.551 Da / Num. of mol.: 130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 26710.363 Da / Num. of mol.: 253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Protein | Mass: 47095.508 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Decorator protein ... , 3 types, 115 molecules ADAOAWAXBFBGBNBOBWBXCFCGCHCPCQDDDODWDXEFEGENEOEWEXFFFGFHFPFQ...
#2: Protein | Mass: 20026.479 Da / Num. of mol.: 75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 21274.934 Da / Num. of mol.: 35 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 28067.344 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: The portal-containing cap of the Borrelia bacteriophage BB1 procapsid Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 16500 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25958 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Details: previous reconstruction / Source name: Other / Type: experimental model |