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- PDB-8hdr: Cyanophage Pam3 neck -

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Basic information

Entry
Database: PDB / ID: 8hdr
TitleCyanophage Pam3 neck
Components
  • Pam3 adaptor protein
  • Pam3 connector protein
  • Pam3 sheath protein
  • Pam3 terminator protein
  • pam3 tube protein
KeywordsVIRAL PROTEIN / fiber / VIRUS
Biological speciesuncultured cyanophage (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsYang, F. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Fine structure and assembly pattern of a minimal myophage Pam3.
Authors: Feng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou /
Abstract: The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
History
DepositionNov 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: pam3 tube protein
2: pam3 tube protein
A: Pam3 connector protein
B: Pam3 connector protein
C: Pam3 connector protein
D: Pam3 connector protein
E: Pam3 connector protein
F: Pam3 connector protein
G: Pam3 terminator protein
H: Pam3 terminator protein
I: Pam3 terminator protein
J: Pam3 terminator protein
K: Pam3 terminator protein
L: Pam3 terminator protein
M: Pam3 sheath protein
N: Pam3 sheath protein
O: Pam3 sheath protein
P: Pam3 sheath protein
Q: Pam3 sheath protein
R: Pam3 sheath protein
S: Pam3 sheath protein
T: Pam3 sheath protein
U: Pam3 sheath protein
V: Pam3 sheath protein
W: Pam3 sheath protein
X: Pam3 sheath protein
Y: pam3 tube protein
Z: pam3 tube protein
a: Pam3 adaptor protein
b: Pam3 adaptor protein
c: Pam3 adaptor protein
d: Pam3 adaptor protein
e: Pam3 adaptor protein
f: Pam3 adaptor protein
g: Pam3 adaptor protein
h: Pam3 adaptor protein
i: Pam3 adaptor protein
j: Pam3 adaptor protein
k: Pam3 adaptor protein
l: Pam3 adaptor protein
m: pam3 tube protein
n: pam3 tube protein
o: pam3 tube protein
p: pam3 tube protein
q: pam3 tube protein
r: pam3 tube protein
s: pam3 tube protein
t: pam3 tube protein
u: pam3 tube protein
v: pam3 tube protein
w: pam3 tube protein
x: pam3 tube protein
y: pam3 tube protein
z: pam3 tube protein


Theoretical massNumber of molelcules
Total (without water)1,122,95454
Polymers1,122,95454
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
pam3 tube protein


Mass: 15293.298 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#2: Protein
Pam3 connector protein


Mass: 12023.414 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#3: Protein
Pam3 terminator protein


Mass: 17682.719 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#4: Protein
Pam3 sheath protein


Mass: 41915.090 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#5: Protein
Pam3 adaptor protein


Mass: 13871.434 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)

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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: Cyanophage Pam3 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: uncultured cyanophage (environmental samples)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Pseudanabaena mucicola
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117851 / Symmetry type: POINT

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