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- EMDB-17672: Middle part of the Borrelia bacteriophage BB1 procapsid, tenfold-... -

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Basic information

Entry
Database: EMDB / ID: EMD-17672
TitleMiddle part of the Borrelia bacteriophage BB1 procapsid, tenfold-symmetrized outer shell
Map data
Sample
  • Complex: Middle part of the Borrelia bacteriophage BB1 procapsid
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Decorator protein P03
    • Protein or peptide: Decorator protein P05
    • Protein or peptide: Scaffold protein
KeywordsBacteriophage / capsid / procapsid / VIRAL PROTEIN
Function / homologyProtein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 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_17672.png

Downloads & links

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Map

FileDownload / File: emd_17672.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 533.504 Å		0.83 Å/pix.
x 640 pix.
= 533.504 Å		0.83 Å/pix.
x 640 pix.
= 533.504 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.01907955 - 0.037332904
Average (Standard dev.)0.00012535029 (±0.002026908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 533.50397 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17672_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_17672_half_map_1.map
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Half map: #1

Fileemd_17672_half_map_2.map
Projections & Slices
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Sample components

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Entire : Middle part of the Borrelia bacteriophage BB1 procapsid

EntireName: Middle part of the Borrelia bacteriophage BB1 procapsid
Components
  • Complex: Middle part of the Borrelia bacteriophage BB1 procapsid
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Decorator protein P03
    • Protein or peptide: Decorator protein P05
    • Protein or peptide: Scaffold protein

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Supramolecule #1: Middle part of the Borrelia bacteriophage BB1 procapsid

SupramoleculeName: Middle part of the Borrelia bacteriophage BB1 procapsid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 36.255551 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MELFDENYYA KAVANIIGEV KDPIMYKWFS PDQIEDVDLQ MGYQKTVKWD AFLNANPTTI ANEVNTISTI GFSSEVVRLN YLKLQYKFR HLKQTSEKFY TSDSYIGDIN NNLLPFAQAY KLASSEIIKL INHFVLTGTV SIQKDGKNQK RLLPNMYGLL N MPEQIKEE ...String:
MELFDENYYA KAVANIIGEV KDPIMYKWFS PDQIEDVDLQ MGYQKTVKWD AFLNANPTTI ANEVNTISTI GFSSEVVRLN YLKLQYKFR HLKQTSEKFY TSDSYIGDIN NNLLPFAQAY KLASSEIIKL INHFVLTGTV SIQKDGKNQK RLLPNMYGLL N MPEQIKEE VASGDKDKMD KIFEKIEAGL SKLELGDEFS TPMMVIVDPA TSLKLVKPYA AAQGAASSCE KWEDVLIQTI KA INNREDV YIETSNLLKH KILIYPLNSE LIKFKPSKYM LPTPNEQVDK DSTDVAHSYI DFVLGGLLAT RKTILQVNIK QS

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Macromolecule #2: Decorator protein P03

MacromoleculeName: Decorator protein P03 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 20.026479 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSDITKIKQE FDKKVAEIQA LMKNPQQDSG LLSNSIDFRD QNLIFSNSGG VCTSSKDKIE NYPAKGYPYK RGVKLSFGDG TTELEVEAG GGDDLYGVCS DIDEFSGMAT VIPITNNFTG YLTLKKDGQN GVNPGDKLNF NQHGELEKVT GAQKSVNAIA L SKAHKLTE DLFIVLASVF GNRAIKG

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Macromolecule #3: Decorator protein P05

MacromoleculeName: Decorator protein P05 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Molecular weightTheoretical: 21.274934 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MGDTTQLVKE YQEKRSKLEK FMKNPQHDAS LLSNSNEFRD KNVEFFASGG TRTSKFDKLE NHPFLGYPYK RGVKRVIQEA QDNQSHYEP HVEAGGGEDL YGICIDIDEF SKTATIVPIT NNFEGYLVAK DSTVKVKDKL IFNKDGALEK VTGAPNKATI N ATALTDAK QISNEVYLVK VAVFGNKAMS RN

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Macromolecule #4: Scaffold protein

MacromoleculeName: Scaffold protein / type: protein_or_peptide / ID: 4 / Number of copies: 15 / 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-HCl
100.0 mMsodium chlorideNaCl
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
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen 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

Startup modelType of model: OTHER / Details: low-pass filtered previous reconstruction
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 29011
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: previous reconstruction
Output model

PDB-8phr:
Middle part of the Borrelia bacteriophage BB1 procapsid, tenfold-symmetrized outer shell

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