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- PDB-9jlf: Cryo-EM Structure of Bacteriophage FCWL1 head-to-tail interface -

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Basic information

Entry
Database: PDB / ID: 9jlf
TitleCryo-EM Structure of Bacteriophage FCWL1 head-to-tail interface
Components
  • Adaptor protein
  • Connector protein
  • Portal protein
  • Tail tube protein
  • Terminator protein
KeywordsVIRAL PROTEIN / T1-like phage / neck / tail
Function / homology
Function and homology information


Phage tail tube protein 3 / Phage tail tube protein, TTP / Protein of unknown function DUF4128 / Phage tail terminator protein / Protein of unknown function DUF4054 / Protein of unknown function (DUF4054) / Protein of unknown function DUF1073 / Phage portal protein
Similarity search - Domain/homology
Portal protein / Terminator protein / Adaptor protein / Tail tube protein / Connector protein
Similarity search - Component
Biological speciesEscherichia phage FCWL1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCai, C. / Wang, Y. / Liu, Y. / Shao, Q. / Wang, A. / Fang, Q.
Funding support China, 2items
OrganizationGrant numberCountry
Other governmentD2301008
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: Structure / Year: 2025
Title: Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage.
Authors: Can Cai / Yueting Wang / Yunshu Liu / Qianqian Shao / Aohan Wang / Lin Li / Yaqi Zheng / Tianyi Zhang / Ziwen Luo / Chongguang Yang / Qianglin Fang /
Abstract: Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1- ...Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1-like phage that belongs to the T1 phage family. We focus on the head, the head-to-tail interface, and its surrounding components. The hexameric capsomer displays unique gaps between neighboring A domains of the major capsid proteins. These gaps are partially filled by the N-loop of the decoration protein, which adopts a unique conformation. These structural features suggest that the phage might employ a novel strategy for stabilizing its head. Furthermore, despite being a siphophage, the head and head-to-tail connector of the phage show high structural similarity to those of a myophage. These findings enhance our understanding of the structure, capsid stabilization mechanism, and evolution of phages in the T1 family.
History
DepositionSep 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein


Theoretical massNumber of molelcules
Total (without water)209,0508
Polymers209,0508
Non-polymers00
Water00
1
D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein

D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein

D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein

D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein

D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein

D: Terminator protein
E: Tail tube protein
a: Portal protein
A: Portal protein
F: Tail tube protein
b: Adaptor protein
B: Adaptor protein
C: Connector protein


Theoretical massNumber of molelcules
Total (without water)1,254,30248
Polymers1,254,30248
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein Terminator protein


Mass: 15191.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MU51
#2: Protein Tail tube protein


Mass: 24217.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUP2
#3: Protein Portal protein


Mass: 49969.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MU40
#4: Protein Adaptor protein


Mass: 15827.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUE8
#5: Protein Connector protein


Mass: 13831.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUS4
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: Escherichia phage FCWL1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2-4158-000 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 84600
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74400 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00282218
ELECTRON MICROSCOPYf_angle_d0.553111216
ELECTRON MICROSCOPYf_dihedral_angle_d3.9211106
ELECTRON MICROSCOPYf_chiral_restr0.04412444
ELECTRON MICROSCOPYf_plane_restr0.00414394

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