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- PDB-9toi: gp39 protein from Escherichia phage vB_EcoS_NBD2 -

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Basic information

Entry
Database: PDB / ID: 9toi
Titlegp39 protein from Escherichia phage vB_EcoS_NBD2
ComponentsPutative major tail protein
KeywordsVIRAL PROTEIN / vB_EcoS_NBD2 bacteriophage / bacteriophage tail
Function / homologyPhage tail tube protein 3 / Phage tail tube protein, TTP / Putative major tail protein
Function and homology information
Biological speciesEscherichia phage vB_EcoS_NBD2 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSasnauskas, G. / Tamulaitiene, G. / Poviloniene, S. / Casaite, V. / Meskys, R.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaLithuania
CitationJournal: Protein Sci / Year: 2026
Title: The Lord of the Rings: Cysteine bonds crosslink the tail of siphovirus.
Authors: Simona Povilonienė / Giedrius Sasnauskas / Giedrė Tamulaitienė / Greta Labutytė / Martynas Talaikis / Algirdas Mikšys / Aurelija Zajančkauskaitė / Lidija Truncaitė / Rolandas Meškys / Vida Časaitė
Abstract: Long, non-contractile tails composed of helical hexameric protein repeats that assemble into continuous tubular structures characterize siphoviruses. The siphovirus tail tube protein gp39 contains ...Long, non-contractile tails composed of helical hexameric protein repeats that assemble into continuous tubular structures characterize siphoviruses. The siphovirus tail tube protein gp39 contains two cysteine residues per monomer. Cryo-electron microscopy revealed that these cysteines are oriented toward the interface between the rings, which facilitates the formation of inter-ring disulfide bonds. Phylogenetic analysis revealed that in the phage tail tube protein-3 (PF08813) family, only a single branch, representing approximately 14% of its members, contains disulfide bonds within the tubular structure, indicating a clear evolutionary adaptation to stabilize the structure. Structural characterization of gp39 alongside its homolog gp13, which naturally lacks disulfide crosslinks, provided insight into this stabilization strategy. Both gp39 and gp13 can self-assemble into tubular structures independently of disulfide bond formation. When cysteine residues were inserted into gp13 at the same positions as in gp39, disulfide bonds were formed, as confirmed by Raman spectroscopy. Differential scanning fluorimetry further demonstrated that variants containing disulfide bonds exhibit enhanced thermal stability. These results reveal the evolutionary and structural basis by which disulfide bonds ensure the stability of phage tail structures and establish the fundamental principles for the design of robust, thermally stable protein nanotubes.
History
DepositionDec 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative major tail protein
B: Putative major tail protein
C: Putative major tail protein
D: Putative major tail protein
E: Putative major tail protein
F: Putative major tail protein
G: Putative major tail protein
H: Putative major tail protein
I: Putative major tail protein
J: Putative major tail protein
K: Putative major tail protein
L: Putative major tail protein


Theoretical massNumber of molelcules
Total (without water)292,56412
Polymers292,56412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative major tail protein


Mass: 24380.301 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage vB_EcoS_NBD2 (virus) / Gene: NBD2_39 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A192YAK4
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: Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage vB_EcoS_NBD2 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 890

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraX1.7model fitting
12cryoSPARC4.7.13D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54474 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 94.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001819004
ELECTRON MICROSCOPYf_angle_d0.471626049
ELECTRON MICROSCOPYf_chiral_restr0.04463273
ELECTRON MICROSCOPYf_plane_restr0.00383264
ELECTRON MICROSCOPYf_dihedral_angle_d11.84486291

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