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- PDB-7yfz: Cyanophage Pam3 baseplate proteins -

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Basic information

Entry
Database: PDB / ID: 7yfz
TitleCyanophage Pam3 baseplate proteins
Components
  • (Pam3 baseplate wedge ...) x 2
  • Pam3 hub gp19
  • Pam3 plug gp18
  • Pam3 sheath initiator gp21
  • Pam3 spike gp20
  • Pam3 tube initiator gp17
KeywordsVIRAL PROTEIN / baseplate / VIRUS
Biological speciesuncultured cyanophage (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 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
DepositionJul 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pam3 baseplate wedge gp22
B: Pam3 baseplate wedge gp22
C: Pam3 baseplate wedge gp23
D: Pam3 baseplate wedge gp23
E: Pam3 baseplate wedge gp22
F: Pam3 baseplate wedge gp22
G: Pam3 baseplate wedge gp23
H: Pam3 baseplate wedge gp22
I: Pam3 baseplate wedge gp22
J: Pam3 baseplate wedge gp23
K: Pam3 baseplate wedge gp22
L: Pam3 baseplate wedge gp22
M: Pam3 baseplate wedge gp23
O: Pam3 baseplate wedge gp22
P: Pam3 baseplate wedge gp22
Q: Pam3 baseplate wedge gp22
R: Pam3 baseplate wedge gp22
S: Pam3 baseplate wedge gp23
X: Pam3 sheath initiator gp21
a: Pam3 tube initiator gp17
b: Pam3 tube initiator gp17
c: Pam3 tube initiator gp17
d: Pam3 tube initiator gp17
e: Pam3 tube initiator gp17
f: Pam3 tube initiator gp17
h: Pam3 plug gp18
i: Pam3 plug gp18
j: Pam3 plug gp18
k: Pam3 plug gp18
l: Pam3 plug gp18
m: Pam3 plug gp18
n: Pam3 sheath initiator gp21
o: Pam3 sheath initiator gp21
p: Pam3 sheath initiator gp21
q: Pam3 sheath initiator gp21
r: Pam3 sheath initiator gp21
t: Pam3 hub gp19
u: Pam3 hub gp19
v: Pam3 hub gp19
w: Pam3 spike gp20
x: Pam3 spike gp20
y: Pam3 spike gp20


Theoretical massNumber of molelcules
Total (without water)968,43842
Polymers968,43842
Non-polymers00
Water00
1


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

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Components

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Pam3 baseplate wedge ... , 2 types, 18 molecules ABEFHIKLOPQRCDGJMS

#1: Protein
Pam3 baseplate wedge gp22


Mass: 32686.787 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#2: Protein
Pam3 baseplate wedge gp23


Mass: 26194.811 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)

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Protein , 5 types, 24 molecules Xnopqrabcdefhijklmtuvwxy

#3: Protein
Pam3 sheath initiator gp21


Mass: 13889.669 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#4: Protein
Pam3 tube initiator gp17


Mass: 19854.342 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#5: Protein
Pam3 plug gp18


Mass: 11724.286 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#6: Protein Pam3 hub gp19


Mass: 25201.736 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)
#7: Protein Pam3 spike gp20


Mass: 23537.537 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) uncultured cyanophage (environmental samples)

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Details

Has protein modificationY

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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: uncultured cyanophage / 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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45155 / Symmetry type: POINT

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