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- PDB-9kmh: The Composite Cryo-EM Structure of the Portal Vertex of Bacteriop... -

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Basic information

Entry
Database: PDB / ID: 9kmh
TitleThe Composite Cryo-EM Structure of the Portal Vertex of Bacteriophage FCWL1
Components
  • Adaptor protein
  • Connector protein
  • Decoration protein
  • Decoration protein gp29
  • Major capsid protein
  • Portal protein
  • Tail tube protein
  • Terminator protein
KeywordsVIRAL PROTEIN / T1-like phage / capsid / icosahedrally averaged
Function / homology
Function and homology information


Phage tail tube protein 3 / Protein of unknown function DUF2184 / Phage tail tube protein, TTP / Major capsid protein / Protein of unknown function DUF4128 / Phage tail terminator protein / Protein of unknown function DUF4054 / : / Protein of unknown function (DUF4054) / Structural cement protein (E217 gp24/Pam3 gp6) ...Phage tail tube protein 3 / Protein of unknown function DUF2184 / Phage tail tube protein, TTP / Major capsid protein / Protein of unknown function DUF4128 / Phage tail terminator protein / Protein of unknown function DUF4054 / : / Protein of unknown function (DUF4054) / Structural cement protein (E217 gp24/Pam3 gp6) / Protein of unknown function DUF1073 / Phage portal protein / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Major capsid protein / IgG-domain-containing decoration protein / Portal protein / Terminator protein / Decoration protein / Adaptor protein / Tail tube protein / Connector protein
Similarity search - Component
Biological speciesEscherichia phage FCWL1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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
DepositionNov 16, 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
aa: Major capsid protein
ab: Decoration protein
ac: Decoration protein
ad: Decoration protein
ae: Decoration protein
af: Major capsid protein
ag: Major capsid protein
ah: Major capsid protein
ai: Major capsid protein
aj: Major capsid protein
al: Decoration protein
am: Decoration protein
an: Major capsid protein
ao: Decoration protein
ap: Decoration protein
aq: Decoration protein
ar: Decoration protein
as: Major capsid protein
at: Major capsid protein
au: Major capsid protein
av: Major capsid protein
aw: Major capsid protein
ay: Decoration protein
az: Decoration protein
ba: Major capsid protein
bb: Decoration protein
bc: Decoration protein
bd: Decoration protein
be: Decoration protein
bf: Major capsid protein
bg: Major capsid protein
bh: Major capsid protein
bi: Major capsid protein
bj: Major capsid protein
bl: Decoration protein
bm: Decoration protein
bn: Major capsid protein
bo: Decoration protein
bp: Decoration protein
bq: Decoration protein
br: Decoration protein
bs: Major capsid protein
bt: Major capsid protein
bu: Major capsid protein
bv: Major capsid protein
bw: Major capsid protein
by: Decoration protein
bz: Decoration protein
ca: Major capsid protein
cb: Decoration protein
cc: Decoration protein
cd: Decoration protein
ce: Decoration protein
cf: Major capsid protein
cg: Major capsid protein
ch: Major capsid protein
ci: Major capsid protein
cj: Major capsid protein
cl: Decoration protein
cm: Decoration protein
cn: Portal protein
co: Portal protein
cp: Portal protein
cq: Portal protein
cr: Terminator protein
cs: Terminator protein
ct: Terminator protein
cu: Terminator protein
cv: Terminator protein
cw: Terminator protein
cx: Adaptor protein
cy: Portal protein
cz: Adaptor protein
da: Adaptor protein
db: Adaptor protein
dc: Adaptor protein
dd: Adaptor protein
de: Adaptor protein
df: Adaptor protein
dg: Adaptor protein
dh: Adaptor protein
di: Adaptor protein
dj: Portal protein
dk: Adaptor protein
dl: Tail tube protein
dm: Tail tube protein
dn: Tail tube protein
do: Tail tube protein
dp: Tail tube protein
dq: Tail tube protein
dr: Connector protein
ds: Connector protein
dt: Connector protein
du: Portal protein
dv: Connector protein
dw: Connector protein
dx: Connector protein
dy: Portal protein
dz: Portal protein
ea: Portal protein
eb: Portal protein
ec: Portal protein
ak: Decoration protein gp29
bk: Decoration protein gp29
bx: Decoration protein gp29
ck: Decoration protein gp29
ax: Decoration protein gp29


Theoretical massNumber of molelcules
Total (without water)2,810,481107
Polymers2,810,481107
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 107 molecules aaafagahaiajanasatauavawbabfbgbhbibjbnbsbtbubvbwcacfcgchcicj...

#1: Protein ...
Major capsid protein / Major capsid protein gp30


Mass: 35301.375 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MTV7
#2: Protein ...
Decoration protein / Decoration protein gp28


Mass: 17022.135 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUC4
#3: Protein
Portal protein / Portal protein gp25


Mass: 49969.102 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MU40
#4: Protein
Terminator protein / Terminator protein gp35


Mass: 15191.521 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MU51
#5: Protein
Adaptor protein / Adaptor protein gp32


Mass: 15827.354 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUE8
#6: Protein
Tail tube protein / Tail tube protein gp36


Mass: 24217.180 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUP2
#7: Protein
Connector protein / Connector protein gp33


Mass: 13831.523 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MUS4
#8: Protein
Decoration protein gp29


Mass: 26355.309 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia phage FCWL1 (virus) / References: UniProt: A0AAX4MTZ1

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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: 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: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 74400 / Symmetry type: POINT

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