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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 Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae
Authors: Mietzsch, M. / Kailasan, S. / Bennett, A. / Chipman, P. / Bentley, F. / Huiskonen, J.T. / Clarke, I.N. / McKenna, R.
History
DepositionJun 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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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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