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- PDB-9cgm: The Structure of Spiroplasma Virus 4 -

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Basic information

Entry
Database: PDB / ID: 9cgm
TitleThe Structure of Spiroplasma Virus 4
Components
  • Capsid protein VP1
  • DNA binding protein ORF8
KeywordsVIRUS / Microviridae / bacteriophage / capsid / Spiroplasma virus 4 / SpV4
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsMietzsch, M. / McKenna, R.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
0: DNA binding protein ORF8
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
e: Capsid protein VP1
f: Capsid protein VP1
g: Capsid protein VP1
h: Capsid protein VP1
i: Capsid protein VP1
j: Capsid protein VP1
k: Capsid protein VP1
l: Capsid protein VP1
m: Capsid protein VP1
n: Capsid protein VP1
o: Capsid protein VP1
p: Capsid protein VP1
q: Capsid protein VP1
r: Capsid protein VP1
s: Capsid protein VP1
t: Capsid protein VP1
u: Capsid protein VP1
v: Capsid protein VP1
w: Capsid protein VP1
x: Capsid protein VP1
y: Capsid protein VP1
z: Capsid protein VP1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Capsid protein VP1
8: Capsid protein VP1
9: DNA binding protein ORF8
C2: DNA binding protein ORF8
D2: DNA binding protein ORF8
E2: DNA binding protein ORF8
F2: DNA binding protein ORF8
G2: DNA binding protein ORF8
H2: DNA binding protein ORF8
I2: DNA binding protein ORF8
J2: DNA binding protein ORF8
K2: DNA binding protein ORF8
L2: DNA binding protein ORF8
M2: DNA binding protein ORF8
N2: DNA binding protein ORF8
O2: DNA binding protein ORF8
P2: DNA binding protein ORF8
Q2: DNA binding protein ORF8
R2: DNA binding protein ORF8
S2: DNA binding protein ORF8
T2: DNA binding protein ORF8
U2: DNA binding protein ORF8
V2: DNA binding protein ORF8
W2: DNA binding protein ORF8
X2: DNA binding protein ORF8
Y2: DNA binding protein ORF8
Z2: DNA binding protein ORF8
a2: DNA binding protein ORF8
b2: DNA binding protein ORF8
c2: DNA binding protein ORF8
d2: DNA binding protein ORF8
e2: DNA binding protein ORF8
f2: DNA binding protein ORF8
g2: DNA binding protein ORF8
h2: DNA binding protein ORF8
i2: DNA binding protein ORF8
j2: DNA binding protein ORF8
k2: DNA binding protein ORF8
l2: DNA binding protein ORF8
m2: DNA binding protein ORF8
n2: DNA binding protein ORF8
o2: DNA binding protein ORF8
p2: DNA binding protein ORF8
q2: DNA binding protein ORF8
r2: DNA binding protein ORF8
s2: DNA binding protein ORF8
t2: DNA binding protein ORF8
u2: DNA binding protein ORF8
v2: DNA binding protein ORF8
w2: DNA binding protein ORF8
x2: DNA binding protein ORF8
y2: DNA binding protein ORF8
z2: DNA binding protein ORF8
12: DNA binding protein ORF8
22: DNA binding protein ORF8
32: DNA binding protein ORF8
42: DNA binding protein ORF8
52: DNA binding protein ORF8
62: DNA binding protein ORF8
72: DNA binding protein ORF8
82: DNA binding protein ORF8


Theoretical massNumber of molelcules
Total (without water)4,016,332120
Polymers4,016,332120
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Capsid protein VP1 / VP1


Mass: 62294.344 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiromicrovirus SpV4 / Gene: ORF1 / Production host: Spiroplasma melliferum (bacteria) / Strain (production host): G1 / References: UniProt: P11333
#2: Protein/peptide ...
DNA binding protein ORF8


Mass: 4644.519 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiromicrovirus SpV4 / Gene: ORF8 / Production host: Spiroplasma melliferum (bacteria) / Strain (production host): G1 / References: UniProt: P11340

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Spiromicrovirus SpV4 / Type: VIRUS / Details: SpV4 was propagated in the S. melliferum strain G1 / Entity ID: all / Source: NATURAL
Source (natural)Organism: Spiromicrovirus SpV4
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77204 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009253260
ELECTRON MICROSCOPYf_angle_d0.811343800
ELECTRON MICROSCOPYf_dihedral_angle_d7.703206760
ELECTRON MICROSCOPYf_chiral_restr0.05836420
ELECTRON MICROSCOPYf_plane_restr0.00644820

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