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- PDB-8phs: Bottom cap of the Borrelia bacteriophage BB1 procapsid, fivefold-... -

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Basic information

Entry
Database: PDB / ID: 8phs
TitleBottom cap of the Borrelia bacteriophage BB1 procapsid, fivefold-symmetrized outer shell
Components
  • Decorator protein P03
  • Decorator protein P04
  • Decorator protein P05
  • Major capsid protein
  • Scaffold protein
KeywordsVIRAL PROTEIN / Bacteriophage / capsid / procapsid
Function / homologyProtein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsRumnieks, J. / Fuzik, T. / Tars, K.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/4/20/704European Union
iNEXT-Discovery18826European Union
iNEXT-Discovery24421European Union
CitationJournal: J Mol Biol / Year: 2023
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
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AB: Major capsid protein
AC: Major capsid protein
AD: Decorator protein P03
AF: Decorator protein P05
AH: Scaffold protein
AI: Scaffold protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Decorator protein P04
AN: Decorator protein P05
AO: Decorator protein P03
AP: Scaffold protein
AQ: Scaffold protein
AR: Scaffold protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Decorator protein P05
AW: Decorator protein P03
AX: Decorator protein P03
AY: Scaffold protein
AZ: Scaffold protein
BA: Scaffold protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Decorator protein P05
BF: Decorator protein P03
BG: Decorator protein P03
BH: Scaffold protein
BI: Scaffold protein
BJ: Scaffold protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Decorator protein P03
BO: Decorator protein P03
BP: Decorator protein P05
BQ: Scaffold protein
BR: Scaffold protein
BS: Scaffold protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Decorator protein P03
BX: Decorator protein P03
BY: Decorator protein P05
BZ: Scaffold protein
CA: Scaffold protein
CB: Scaffold protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Decorator protein P03
CG: Decorator protein P03
CH: Decorator protein P03
CI: Scaffold protein
CJ: Scaffold protein
CK: Scaffold protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Decorator protein P05
CP: Decorator protein P03
CQ: Decorator protein P03
CR: Scaffold protein
CS: Scaffold protein
CT: Scaffold protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Scaffold protein
CY: Scaffold protein
CZ: Scaffold protein


Theoretical massNumber of molelcules
Total (without water)2,114,50375
Polymers2,114,50375
Non-polymers00
Water0
1
AB: Major capsid protein
AC: Major capsid protein
AD: Decorator protein P03
AF: Decorator protein P05
AH: Scaffold protein
AI: Scaffold protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Decorator protein P04
AN: Decorator protein P05
AO: Decorator protein P03
AP: Scaffold protein
AQ: Scaffold protein
AR: Scaffold protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Decorator protein P05
AW: Decorator protein P03
AX: Decorator protein P03
AY: Scaffold protein
AZ: Scaffold protein
BA: Scaffold protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Decorator protein P05
BF: Decorator protein P03
BG: Decorator protein P03
BH: Scaffold protein
BI: Scaffold protein
BJ: Scaffold protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Decorator protein P03
BO: Decorator protein P03
BP: Decorator protein P05
BQ: Scaffold protein
BR: Scaffold protein
BS: Scaffold protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Decorator protein P03
BX: Decorator protein P03
BY: Decorator protein P05
BZ: Scaffold protein
CA: Scaffold protein
CB: Scaffold protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Decorator protein P03
CG: Decorator protein P03
CH: Decorator protein P03
CI: Scaffold protein
CJ: Scaffold protein
CK: Scaffold protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Decorator protein P05
CP: Decorator protein P03
CQ: Decorator protein P03
CR: Scaffold protein
CS: Scaffold protein
CT: Scaffold protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Scaffold protein
CY: Scaffold protein
CZ: Scaffold protein
x 5


  • defined by author&software
  • Evidence: electron microscopy, not applicable
  • 10.6 MDa, 375 polymers
Theoretical massNumber of molelcules
Total (without water)10,572,514375
Polymers10,572,514375
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein ...
Major capsid protein


Mass: 36255.551 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Details: Major capsid protein / Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L06 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#2: Protein
Decorator protein P03


Mass: 20026.479 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L03 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#3: Protein
Decorator protein P05


Mass: 21274.934 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: Decorator protein P05 / Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BbuZS7_P05 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#4: Protein ...
Scaffold protein /


Mass: 26710.363 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L02 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q9R2Q2
#5: Protein Decorator protein P04


Mass: 28067.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L04 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Top cap of the Borrelia bacteriophage BB1 procapsid / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21-AI
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClTris1
2100 mMsodium chlorideNaClSodium chloride1
310 mMmagnesium sulfateMgSO41
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1RELION3.1.3particle selection
4Gctf1.18CTF correction
7Coot0.9.8.4model fitting
9RELION3.1.3initial Euler assignment
10RELION3.1.3final Euler assignment
12RELION3.1.33D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25958 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDDetailsSource nameType
11previous reconstructionOtherexperimental model
21AlphaFoldin silico model

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