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- EMDB-40674: Subtomogram average of immature PhiKZ Major Capsid Protein from t... -

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Basic information

Entry
Database: EMDB / ID: EMD-40674
TitleSubtomogram average of immature PhiKZ Major Capsid Protein from tubular arrays
Map data
Sample
  • Complex: Immature PhiKZ major capsid protein in a tubular array
    • Protein or peptide: PhiKZ major capsid protein
Keywordsmajor capsid protein / HK97-fold / VIRAL PROTEIN
Function / homologyviral capsid / Major capsid protein
Function and homology information
Biological speciesPhikzvirus phiKZ
Methodsubtomogram averaging / cryo EM / Resolution: 13.0 Å
AuthorsLaughlin TG / Villa E
Funding support United States, 4 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129245 United States
National Science Foundation (NSF, United States)NSF DBI 1920374 United States
Simons Foundation United States
CitationJournal: Science / Year: 2024
Title: An intron endonuclease facilitates interference competition between coinfecting viruses.
Authors: Erica A Birkholz / Chase J Morgan / Thomas G Laughlin / Rebecca K Lau / Amy Prichard / Sahana Rangarajan / Gabrielle N Meza / Jina Lee / Emily Armbruster / Sergey Suslov / Kit Pogliano / ...Authors: Erica A Birkholz / Chase J Morgan / Thomas G Laughlin / Rebecca K Lau / Amy Prichard / Sahana Rangarajan / Gabrielle N Meza / Jina Lee / Emily Armbruster / Sergey Suslov / Kit Pogliano / Justin R Meyer / Elizabeth Villa / Kevin D Corbett / Joe Pogliano /
Abstract: Introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in ...Introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. In this work, we studied intron-encoded homing endonuclease gp210 in bacteriophage ΦPA3 and found that it contributes to viral competition by interfering with the replication of a coinfecting phage, ΦKZ. We show that gp210 targets a specific sequence in ΦKZ, which prevents the assembly of progeny viruses. This work demonstrates how a homing endonuclease can be deployed in interference competition among viruses and provide a relative fitness advantage. Given the ubiquity of homing endonucleases, this selective advantage likely has widespread evolutionary implications in diverse plasmid and viral competition as well as virus-host interactions.
History
DepositionMay 1, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40674.png

Downloads & links

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Map

FileDownload / File: emd_40674.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.46 Å/pix.
x 128 pix.
= 442.496 Å		3.46 Å/pix.
x 128 pix.
= 442.496 Å		3.46 Å/pix.
x 128 pix.
= 442.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.457 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.28038615 - 0.38181207
Average (Standard dev.)0.00208719 (±0.093099475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 442.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40674_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40674_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40674_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Immature PhiKZ major capsid protein in a tubular array

EntireName: Immature PhiKZ major capsid protein in a tubular array
Components
  • Complex: Immature PhiKZ major capsid protein in a tubular array
    • Protein or peptide: PhiKZ major capsid protein

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Supramolecule #1: Immature PhiKZ major capsid protein in a tubular array

SupramoleculeName: Immature PhiKZ major capsid protein in a tubular array
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Phikzvirus phiKZ

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Macromolecule #1: PhiKZ major capsid protein

MacromoleculeName: PhiKZ major capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
SequenceString: MSVHALRELF KHKGEKNYEV FSMEDFIGRL ESEIGLNDSV VSQGRSLISS ISHENFGTVQ ATDIQDAAAI YNKMQMLVND YGFERVSSSD PQVRAREERV RENQITAATM AAIACADETK YIRALRGITK AKASNEDHVK VVQHQFNGPA GGIQVFENGV GLENYNEKSQ ...String:
MSVHALRELF KHKGEKNYEV FSMEDFIGRL ESEIGLNDSV VSQGRSLISS ISHENFGTVQ ATDIQDAAAI YNKMQMLVND YGFERVSSSD PQVRAREERV RENQITAATM AAIACADETK YIRALRGITK AKASNEDHVK VVQHQFNGPA GGIQVFENGV GLENYNEKSQ RDFRVVTIGY NLAASRQDEF AERIYPTTVI NPIEGGVVQV LPYIAVMKDV YHEVSGVKMD NEEVNMVEAY RDPSILDDES IALIPALDPA GSNADFFVDP ALVPPYTIKN EQNLTITTAP LKANVRLDLM GNSNANLLIQ RGMLEVSDTI DPAGRLKNLF VLLGGKVVKF KVDRLPRAVF QPDLVGDTRN AVIRFDSDDL VVSGDTTFID GSADGVINDL KTAKLSLRLS VGFGGTISLS KGDSKFGATD TYVDKVLNED GQVMDNADPA VKAILDQLTD LAVIGFELDT RFTNTNRRQR GHLLQTRALQ FRHPIPMHAP VTLPMDTMTD EGPGEVVKAL TVNTNIRNSN NAVKRMLNYL AQLREVVHNG YNRPKFGIIE GALSAVMRPT YRYKELDLEK VIDTIKSKDR WDDVCAAILN CVKAELFPAH RDSNIEAAFR VISGNQDETP MYLFCSDKEI ANYLMTKGDD RTLGAYLKYD IVSTNNQLFD GKLVVIPTRA VQQENDILSW GQFFYVSTVI ADLPITRGGH QVTREIAAIP FNLHVNNIPF ALEFKITGFQ KVMGETQFNG KLADLKP

UniProtKB: Major capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsP. aeruginosa cells expressing PhiPA3 gp210-GFPmut1 infected with PhiKZ

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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 / Number real images: 1 / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number subtomograms used: 21121
ExtractionNumber tomograms: 14 / Number images used: 60000 / Software: (Name: Dynamo (ver. 1.1514), Warp (ver. 1.09))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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