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- EMDB-13664: GA1 bacteriophage portal protein -

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Basic information

Entry
Database: EMDB / ID: EMD-13664
TitleGA1 bacteriophage portal protein
Map data
Sample
  • Complex: GA1 bacteriophage portal protein
    • Protein or peptide: Head-tail connector (Portal protein)
KeywordsBacteriophage / Portal protein / cryoEM / VIRAL PROTEIN
Function / homologyPortal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Head-tail connector (Portal protein)
Function and homology information
Biological speciesBacillus phage GA-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJaved A / Villanueva H
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009513 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R002622/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Viruses / Year: 2021
Title: Cryo-EM Structures of Two Bacteriophage Portal Proteins Provide Insights for Antimicrobial Phage Engineering.
Authors: Abid Javed / Hugo Villanueva / Shadikejiang Shataer / Sara Vasciaveo / Renos Savva / Elena V Orlova /
Abstract: Widespread antibiotic resistance has returned attention to bacteriophages as a means of managing bacterial pathogenesis. Synthetic biology approaches to engineer phages have demonstrated genomic ...Widespread antibiotic resistance has returned attention to bacteriophages as a means of managing bacterial pathogenesis. Synthetic biology approaches to engineer phages have demonstrated genomic editing to broaden natural host ranges, or to optimise microbicidal action. Gram positive pathogens cause serious pastoral animal and human infections that are especially lethal in newborns. Such pathogens are targeted by the obligate lytic phages of the and families. These phages have relatively small ~20 kb linear protein-capped genomes and their compact organisation, relatively few structural elements, and broad host range, are appealing from a phage-engineering standpoint. In this study, we focus on portal proteins, which are core elements for the assembly of such tailed phages. The structures of dodecameric portal complexes from phage GA1, which targets , and phage phiCPV4 that infects , were determined at resolutions of 3.3 Å and 2.9 Å, respectively. Both are found to closely resemble the related phi29 portal protein fold. However, the portal protein of phiCPV4 exhibits interesting differences in the clip domain. These structures provide new insights on structural diversity in portal proteins and will be essential for considerations in phage structural engineering.
History
DepositionOct 1, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13664.png

Downloads & links

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Map

FileDownload / File: emd_13664.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.06340552 - 0.117885455
Average (Standard dev.)0.00017367245 (±0.0038323547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GA1 bacteriophage portal protein

EntireName: GA1 bacteriophage portal protein
Components
  • Complex: GA1 bacteriophage portal protein
    • Protein or peptide: Head-tail connector (Portal protein)

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Supramolecule #1: GA1 bacteriophage portal protein

SupramoleculeName: GA1 bacteriophage portal protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: A dodecamer complex made up of 12 subunits.
Source (natural)Organism: Bacillus phage GA-1 (virus)

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Macromolecule #1: Head-tail connector (Portal protein)

MacromoleculeName: Head-tail connector (Portal protein) / type: protein_or_peptide / ID: 1
Details: In each subunit of the dodecamer, the DNA Tunnel loop residues (232 - 250) has not been modelled due to lack of EM density. Also missing in the pdb structure are 22 residues at the C- ...Details: In each subunit of the dodecamer, the DNA Tunnel loop residues (232 - 250) has not been modelled due to lack of EM density. Also missing in the pdb structure are 22 residues at the C-terminus and 7 residues at the N-terminus in each chain.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage GA-1 (virus)
Molecular weightTheoretical: 35.307801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLEDGFSYKT IGEIQRRRGN LWFRTYQRYL FSLAYQMFEW QGLPKTVDPI FLEKQLHQRG FVAFYKDEMY GYLGVQGTLS GQINLYNQP NFYTASAPTY QKSFPLYWYD MGEDLNEKGQ GIVIYNNLER MPTLDILNLY AMNLAELKET IYVNQNAQKT P VIIKAGDN ...String:
MLEDGFSYKT IGEIQRRRGN LWFRTYQRYL FSLAYQMFEW QGLPKTVDPI FLEKQLHQRG FVAFYKDEMY GYLGVQGTLS GQINLYNQP NFYTASAPTY QKSFPLYWYD MGEDLNEKGQ GIVIYNNLER MPTLDILNLY AMNLAELKET IYVNQNAQKT P VIIKAGDN DLFSMKQVYN KYEGNEPVIF AGKKFNTDDI EVLKTDAPYV ADKLTMLFKD QWNEAMTFLG LSNANTDKKE RL IQSEVES NNDQIQGSAN IYLAPRQEAC RLINEYYGLN VSVKLRKELV GNGELHNAIE GNSGMGNTV

UniProtKB: Head-tail connector (Portal 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

Concentration0.05 mg/mL
BufferpH: 7.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: 3ul of sample was applied on lacey carbon grids..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 95.0 K / Max: 98.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-12 / Number grids imaged: 1 / Number real images: 2249 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
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

Particle selectionNumber selected: 50466
Startup modelType of model: OTHER / Details: Initial 3D map derived from negative stain data.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 22456
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1fou


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 97.7 / Target criteria: Correlation coefficient
Output model

PDB-7pv2:
GA1 bacteriophage portal protein

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