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- PDB-7x30: Capsid structure of Staphylococcus jumbo bacteriophage S6 -

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Basic information

Entry
Database: PDB / ID: 7x30
TitleCapsid structure of Staphylococcus jumbo bacteriophage S6
Components
  • Hoc-like protein ORF90
  • Major structural protein ORF12
KeywordsVIRUS / Phage / Phage head / CryoEM / Bacteriophage / Cryo-EM
Biological speciesStaphylococcus phage S6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKoibuchi, W. / Uchiyama, J. / Matsuzaki, S. / Murata, K. / Iwasaki, K. / Miyazaki, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K18521 Japan
Japan Society for the Promotion of Science (JSPS)18K06154 Japan
CitationJournal: To Be Published
Title: Capsid structure of Staphylococcus jumbo bacteriophage S6
Authors: Koibuchi, W. / Uchiyama, J. / Matsuzaki, S. / Murata, K. / Iwasaki, K. / Miyazaki, N.
History
DepositionFeb 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major structural protein ORF12
a: Major structural protein ORF12
b: Major structural protein ORF12
c: Major structural protein ORF12
d: Major structural protein ORF12
e: Major structural protein ORF12
f: Major structural protein ORF12
g: Major structural protein ORF12
h: Major structural protein ORF12
i: Major structural protein ORF12
j: Major structural protein ORF12
k: Major structural protein ORF12
l: Major structural protein ORF12
m: Major structural protein ORF12
n: Major structural protein ORF12
o: Major structural protein ORF12
p: Major structural protein ORF12
q: Major structural protein ORF12
r: Major structural protein ORF12
s: Major structural protein ORF12
t: Major structural protein ORF12
u: Major structural protein ORF12
v: Major structural protein ORF12
w: Major structural protein ORF12
x: Major structural protein ORF12
y: Major structural protein ORF12
z: Major structural protein ORF12
P: Hoc-like protein ORF90
Q: Hoc-like protein ORF90
R: Hoc-like protein ORF90
S: Hoc-like protein ORF90


Theoretical massNumber of molelcules
Total (without water)1,812,60231
Polymers1,812,60231
Non-polymers00
Water00
1
A: Major structural protein ORF12
a: Major structural protein ORF12
b: Major structural protein ORF12
c: Major structural protein ORF12
d: Major structural protein ORF12
e: Major structural protein ORF12
f: Major structural protein ORF12
g: Major structural protein ORF12
h: Major structural protein ORF12
i: Major structural protein ORF12
j: Major structural protein ORF12
k: Major structural protein ORF12
l: Major structural protein ORF12
m: Major structural protein ORF12
n: Major structural protein ORF12
o: Major structural protein ORF12
p: Major structural protein ORF12
q: Major structural protein ORF12
r: Major structural protein ORF12
s: Major structural protein ORF12
t: Major structural protein ORF12
u: Major structural protein ORF12
v: Major structural protein ORF12
w: Major structural protein ORF12
x: Major structural protein ORF12
y: Major structural protein ORF12
z: Major structural protein ORF12
P: Hoc-like protein ORF90
Q: Hoc-like protein ORF90
R: Hoc-like protein ORF90
S: Hoc-like protein ORF90
x 60


  • complete icosahedral assembly
  • Evidence: electron microscopy
  • 109 MDa, 1860 polymers
Theoretical massNumber of molelcules
Total (without water)108,756,1251860
Polymers108,756,1251860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major structural protein ORF12
a: Major structural protein ORF12
b: Major structural protein ORF12
c: Major structural protein ORF12
d: Major structural protein ORF12
e: Major structural protein ORF12
f: Major structural protein ORF12
g: Major structural protein ORF12
h: Major structural protein ORF12
i: Major structural protein ORF12
j: Major structural protein ORF12
k: Major structural protein ORF12
l: Major structural protein ORF12
m: Major structural protein ORF12
n: Major structural protein ORF12
o: Major structural protein ORF12
p: Major structural protein ORF12
q: Major structural protein ORF12
r: Major structural protein ORF12
s: Major structural protein ORF12
t: Major structural protein ORF12
u: Major structural protein ORF12
v: Major structural protein ORF12
w: Major structural protein ORF12
x: Major structural protein ORF12
y: Major structural protein ORF12
z: Major structural protein ORF12
P: Hoc-like protein ORF90
Q: Hoc-like protein ORF90
R: Hoc-like protein ORF90
S: Hoc-like protein ORF90
x 5


  • icosahedral pentamer
  • 9.06 MDa, 155 polymers
Theoretical massNumber of molelcules
Total (without water)9,063,010155
Polymers9,063,010155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major structural protein ORF12
a: Major structural protein ORF12
b: Major structural protein ORF12
c: Major structural protein ORF12
d: Major structural protein ORF12
e: Major structural protein ORF12
f: Major structural protein ORF12
g: Major structural protein ORF12
h: Major structural protein ORF12
i: Major structural protein ORF12
j: Major structural protein ORF12
k: Major structural protein ORF12
l: Major structural protein ORF12
m: Major structural protein ORF12
n: Major structural protein ORF12
o: Major structural protein ORF12
p: Major structural protein ORF12
q: Major structural protein ORF12
r: Major structural protein ORF12
s: Major structural protein ORF12
t: Major structural protein ORF12
u: Major structural protein ORF12
v: Major structural protein ORF12
w: Major structural protein ORF12
x: Major structural protein ORF12
y: Major structural protein ORF12
z: Major structural protein ORF12
P: Hoc-like protein ORF90
Q: Hoc-like protein ORF90
R: Hoc-like protein ORF90
S: Hoc-like protein ORF90
x 6


  • icosahedral 23 hexamer
  • 10.9 MDa, 186 polymers
Theoretical massNumber of molelcules
Total (without water)10,875,613186
Polymers10,875,613186
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein ...
Major structural protein ORF12


Mass: 59259.133 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage S6 (virus)
#2: Protein
Hoc-like protein ORF90


Mass: 53151.375 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage S6 (virus)

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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: Staphylococcus phage S6 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus phage S6 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Virus shellName: Head / Diameter: 1300 nm / Triangulation number (T number): 27
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 1000 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27164 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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