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- EMDB-17670: Portal from the Borrelia bacteriophage BB1 procapsid with bound s... -

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Basic information

Entry
Database: EMDB / ID: EMD-17670
TitlePortal from the Borrelia bacteriophage BB1 procapsid with bound scaffold protein
Map data
Sample
  • Complex: Portal with bound scaffold protein
    • Protein or peptide: Phage portal protein
    • Protein or peptide: Scaffold protein
KeywordsBacteriophage / portal / DNA packaging / scaffold / VIRAL PROTEIN
Function / homologyUncharacterised 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
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsRumnieks J / Fuzik T / Tars K
Funding supportEuropean Union, 3 items
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, 2023-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17670.png

Downloads & links

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Map

FileDownload / File: emd_17670.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8336 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.013060118 - 0.03435946
Average (Standard dev.)0.00028703266 (±0.0016695558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.75198 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17670_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17670_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17670_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Portal with bound scaffold protein

EntireName: Portal with bound scaffold protein
Components
  • Complex: Portal with bound scaffold protein
    • Protein or peptide: Phage portal protein
    • Protein or peptide: Scaffold protein

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Supramolecule #1: Portal with bound scaffold protein

SupramoleculeName: Portal with bound scaffold protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)

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Macromolecule #1: Phage portal protein

MacromoleculeName: Phage portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 47.095508 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MCDLRKTKLI DKISSLELYK YSIFFRNYIE NVAEDCLKNG LILESAAHNV SEVELARLKV QLKNALLNCI ISYRFHGIGY VLVKTKDTL IDLEQPVNIE LPIGFEYLDY EYVRDLGVDF DHITYKVKSN NKNNSLDAVK IHKSRLIIYE NFDYILKRYV P CYTESFLL ...String:
MCDLRKTKLI DKISSLELYK YSIFFRNYIE NVAEDCLKNG LILESAAHNV SEVELARLKV QLKNALLNCI ISYRFHGIGY VLVKTKDTL IDLEQPVNIE LPIGFEYLDY EYVRDLGVDF DHITYKVKSN NKNNSLDAVK IHKSRLIIYE NFDYILKRYV P CYTESFLL DIYLFEKIYV EIERRIENHN FLFYKDESLV QLQDALSSAT TSLSALTQSN NDRGSGILSS FLRKQNSNNH SK DISNLRN LNDSLSQELA RLKSNLNNEG MFYTATPSAS LEVIKYDLSY LKEALALIKA KIGADTKEPL TRSFNEQAKG LGN DGKGDR SNYYDFLKGV QEQVENSCNL KLTKYFGLDM KFNSLIMLSE EQKVERDIKL IELYSKYNQL IQSSSFNNEE LAML KEKLF SF

UniProtKB: Phage portal protein

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Macromolecule #2: Scaffold protein

MacromoleculeName: Scaffold protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 26.710363 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
100.0 mMsodium chlorideNaClSodium chloride
10.0 mMmagnesium sulfateMgSO4
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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

Startup modelType of model: OTHER / Details: De novo SGD model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 37938
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: experimental modelmodel from previous reconstruction
Output model

PDB-8php:
Portal from the Borrelia bacteriophage BB1 procapsid with bound scaffold protein

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