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- EMDB-45583: The Structure of Spiroplasma Virus 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-45583
TitleThe Structure of Spiroplasma Virus 4
Map data
Sample
  • Virus: Spiromicrovirus SpV4
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: DNA binding protein ORF8
KeywordsMicroviridae / bacteriophage / capsid / Spiroplasma virus 4 / SpV4 / VIRUS
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / structural molecule activity / DNA binding
Similarity search - Function
Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Capsid protein VP1 / DNA binding protein ORF8
Similarity search - Component
Biological speciesSpiromicrovirus SpV4
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsMietzsch M / McKenna R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2024
Title: The Structure of : Exploring the Capsid Diversity of the .
Authors: Mario Mietzsch / Shweta Kailasan / Antonette Bennett / Paul Chipman / Bentley Fane / Juha T Huiskonen / Ian N Clarke / Robert McKenna /
Abstract: (SpV4) is a bacteriophage of the , which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure ... (SpV4) is a bacteriophage of the , which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy to a resolution of 2.5 Å. A striking feature of the SpV4 capsid is the mushroom-like protrusions at the 3-fold axes, which is common among all members of the subfamily While the function of the protrusion is currently unknown, this feature varies widely in this subfamily and is therefore possibly an adaptation for host recognition. Furthermore, on the interior of the SpV4 capsid, the location of DNA-binding protein VP8 was identified and shown to have low structural conservation to the capsids of other viruses in the family. The structural characterization of SpV4 will aid future studies analyzing the virus-host interaction, to understand disease mechanisms at a molecular level. Furthermore, the structural comparisons in this study, including a low-resolution structure of the chlamydia phage 2, provide an overview of the structural repertoire of the viruses in this family that infect various bacterial hosts, which in turn infect a wide range of animals and plants.
History
DepositionJun 30, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45583.png

Downloads & links

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Map

FileDownload / File: emd_45583.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.06 Å/pix.
x 550 pix.
= 583.55 Å		1.06 Å/pix.
x 550 pix.
= 583.55 Å		1.06 Å/pix.
x 550 pix.
= 583.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-14.781516 - 23.707332999999998
Average (Standard dev.)0.000000001860729 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-275-275-275
Dimensions550550550
Spacing550550550
CellA=B=C: 583.55 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45583_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_45583_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Spiromicrovirus SpV4

EntireName: Spiromicrovirus SpV4
Components
  • Virus: Spiromicrovirus SpV4
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: DNA binding protein ORF8

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Supramolecule #1: Spiromicrovirus SpV4

SupramoleculeName: Spiromicrovirus SpV4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: SpV4 was propagated in the S. melliferum strain G1 / NCBI-ID: 10855 / Sci species name: Spiromicrovirus SpV4 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Spiromicrovirus SpV4
Molecular weightTheoretical: 62.294344 KDa
Recombinant expressionOrganism: Spiroplasma melliferum (bacteria)
SequenceString: MKKKMSKLNA RVHDFSMFKG NHIPRSKIHI PHKTIRAFNV GEIIPIYQTP VYPGEHIKMD LTSLYRPSTF IVPPMDDLIV DTYAFAVPW RIVWKDLEKF FGENSDSWDV KNAPPVPDIV APSGGWDYGT LADHFGITPK VPGIRVKSLR FRAYAKIIND W FRDQNLSS ...String:
MKKKMSKLNA RVHDFSMFKG NHIPRSKIHI PHKTIRAFNV GEIIPIYQTP VYPGEHIKMD LTSLYRPSTF IVPPMDDLIV DTYAFAVPW RIVWKDLEKF FGENSDSWDV KNAPPVPDIV APSGGWDYGT LADHFGITPK VPGIRVKSLR FRAYAKIIND W FRDQNLSS ECALTLDSSN SQGSNGSNQV TDIQLGGKPY IANKYHDYFT SCLPAPQKGA PTTLNVGGMA PVTTKFRDVP NL SGTPLIF RDNKGRTIKT GQLGIGPVDA GFLVAQNTAQ AANGERAIPS NLWADLSNAT GISISDLRLA ITYQHYKEMD ARG GTRYVE FTLNHFGVHT ADARLQRSEF LGGHSQSLLV QSVPQTSSTV EKMTPQGNLA AFSETMIQNN YLVNKTFTEH SYII VLAVV RYKHTYQQGI EADWFRGQDK FDMYDPLLAN ISEQPVKNRE IMVQGNSQDN EIFGFQEAWA DLRFKPNSVA GVMRS SHPQ SLDYWHFADH YAQLPKLSSE WLKEDYKNVD RTLALKASDN TPQLRVDFMF NTIAEKPMPL YSTPGLRRI

UniProtKB: Capsid protein VP1

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Macromolecule #2: DNA binding protein ORF8

MacromoleculeName: DNA binding protein ORF8 / type: protein_or_peptide / ID: 2 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Spiromicrovirus SpV4
Molecular weightTheoretical: 4.644519 KDa
Recombinant expressionOrganism: Spiroplasma melliferum (bacteria)
SequenceString:
MRRKVKNTKR HQWRLTHSAR SIKRANIMPS NPRGGRRF

UniProtKB: DNA binding protein ORF8

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77204
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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