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- PDB-9lna: SFP21A phage tail fiber (Gp09) -

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Basic information

Entry
Database: PDB / ID: 9lna
TitleSFP21A phage tail fiber (Gp09)
ComponentsTail fibers protein
KeywordsVIRAL PROTEIN / Shigella flexneri / bacteriophage / tail fiber / Podoviridae
Function / homology
Function and homology information


virus tail / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
Biological speciesShigella phage SFP21A (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBaek, Y. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the tail fiber protein from Podoviridae family bacteriophage infecting Shigella flexneri
Authors: Baek, Y. / Choi, H. / Lee, J. / Ha, N.-C.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail fibers protein
B: Tail fibers protein
C: Tail fibers protein


Theoretical massNumber of molelcules
Total (without water)273,8793
Polymers273,8793
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, shown in EM data
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Tail fibers protein


Mass: 91293.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage SFP21A (virus) / Gene: SFP21A_009 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAE9VVY9
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: Trimeric complex of phage tail fiber / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.118 MDa / Experimental value: YES
Source (natural)Organism: Shigella flexneri (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146100 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214469
ELECTRON MICROSCOPYf_angle_d0.55519674
ELECTRON MICROSCOPYf_dihedral_angle_d6.3012022
ELECTRON MICROSCOPYf_chiral_restr0.0412064
ELECTRON MICROSCOPYf_plane_restr0.0042553

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