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- PDB-8y6v: Near-atomic structure of icosahedrally averaged jumbo bacteriopha... -

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Basic information

Entry
Database: PDB / ID: 8y6v
TitleNear-atomic structure of icosahedrally averaged jumbo bacteriophage PhiKZ capsid
Components
  • gp119
  • gp120
  • gp162
  • gp184
  • gp244
  • gp28
  • gp35
  • gp85
  • gp86
  • gp91
  • gp93
KeywordsVIRUS / phiKZ / capsid protein / viral assembly / Pseudomonas aeruginosa / jumbo phage
Biological speciesPhikzvirus phiKZ
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang, Y. / Shao, Q. / Guo, M. / Han, L. / Zhao, X. / Wang, A. / Li, X. / Wang, B. / Pan, J. / Chen, Z. ...Yang, Y. / Shao, Q. / Guo, M. / Han, L. / Zhao, X. / Wang, A. / Li, X. / Wang, B. / Pan, J. / Chen, Z. / Fokine, A. / Sun, L. / Fang, Q.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2302500 China
Shenzhen Medical Research FundD2301008 China
Shenzhen Science and Technology ProgramZDSYS20230626091203007 China
R&D Program of Guangzhou LaboratorySRPG22-003 China
CitationJournal: Nat Commun / Year: 2024
Title: Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages.
Authors: Yashan Yang / Qianqian Shao / Mingcheng Guo / Lin Han / Xinyue Zhao / Aohan Wang / Xiangyun Li / Bo Wang / Ji-An Pan / Zhenguo Chen / Andrei Fokine / Lei Sun / Qianglin Fang /
Abstract: Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic ...Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.
History
DepositionFeb 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: gp28
B: gp35
E: gp85
F: gp85
G: gp86
H: gp91
K: gp93
L: gp93
M: gp93
J: gp119
a: gp120
b: gp120
c: gp120
d: gp120
e: gp120
f: gp120
g: gp120
h: gp120
i: gp120
j: gp120
k: gp120
l: gp120
m: gp120
n: gp120
o: gp120
p: gp120
q: gp120
r: gp120
s: gp120
t: gp120
u: gp120
v: gp120
w: gp120
x: gp120
y: gp120
z: gp120
A: gp120
N: gp162
O: gp162
P: gp162
I: gp184
C: gp244


Theoretical massNumber of molelcules
Total (without water)2,785,49842
Polymers2,785,49842
Non-polymers00
Water00
1
D: gp28
B: gp35
E: gp85
F: gp85
G: gp86
H: gp91
K: gp93
L: gp93
M: gp93
J: gp119
a: gp120
b: gp120
c: gp120
d: gp120
e: gp120
f: gp120
g: gp120
h: gp120
i: gp120
j: gp120
k: gp120
l: gp120
m: gp120
n: gp120
o: gp120
p: gp120
q: gp120
r: gp120
s: gp120
t: gp120
u: gp120
v: gp120
w: gp120
x: gp120
y: gp120
z: gp120
A: gp120
N: gp162
O: gp162
P: gp162
I: gp184
C: gp244
x 60


  • complete icosahedral assembly
  • Evidence: electron microscopy, not applicable
  • 167 MDa, 2520 polymers
Theoretical massNumber of molelcules
Total (without water)167,129,8912520
Polymers167,129,8912520
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
D: gp28
B: gp35
E: gp85
F: gp85
G: gp86
H: gp91
K: gp93
L: gp93
M: gp93
J: gp119
a: gp120
b: gp120
c: gp120
d: gp120
e: gp120
f: gp120
g: gp120
h: gp120
i: gp120
j: gp120
k: gp120
l: gp120
m: gp120
n: gp120
o: gp120
p: gp120
q: gp120
r: gp120
s: gp120
t: gp120
u: gp120
v: gp120
w: gp120
x: gp120
y: gp120
z: gp120
A: gp120
N: gp162
O: gp162
P: gp162
I: gp184
C: gp244
x 5


  • icosahedral pentamer
  • 13.9 MDa, 210 polymers
Theoretical massNumber of molelcules
Total (without water)13,927,491210
Polymers13,927,491210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
D: gp28
B: gp35
E: gp85
F: gp85
G: gp86
H: gp91
K: gp93
L: gp93
M: gp93
J: gp119
a: gp120
b: gp120
c: gp120
d: gp120
e: gp120
f: gp120
g: gp120
h: gp120
i: gp120
j: gp120
k: gp120
l: gp120
m: gp120
n: gp120
o: gp120
p: gp120
q: gp120
r: gp120
s: gp120
t: gp120
u: gp120
v: gp120
w: gp120
x: gp120
y: gp120
z: gp120
A: gp120
N: gp162
O: gp162
P: gp162
I: gp184
C: gp244
x 6


  • icosahedral 23 hexamer
  • 16.7 MDa, 252 polymers
Theoretical massNumber of molelcules
Total (without water)16,712,989252
Polymers16,712,989252
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

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Components

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Protein , 11 types, 42 molecules DBEFGHKLMJabcdefghijklmnopqrst...

#1: Protein gp28


Mass: 36511.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#2: Protein gp35


Mass: 29713.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#3: Protein gp85


Mass: 16438.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#4: Protein gp86


Mass: 48893.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#5: Protein gp91


Mass: 20817.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#6: Protein gp93


Mass: 47656.105 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#7: Protein gp119


Mass: 20253.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#8: Protein ...
gp120


Mass: 83022.883 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#9: Protein gp162


Mass: 57705.137 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#10: Protein gp184


Mass: 25300.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ
#11: Protein gp244


Mass: 13427.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phikzvirus phiKZ

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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: Phikzvirus phiKZ / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Phikzvirus phiKZ
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa
Virus shellTriangulation number (T number): 27
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: EMS Lacey Carbon
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 magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 903900 / Symmetry type: POINT

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