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- EMDB-56097: gp13 protein from vB_PagS_MED16 bacteriophage -

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Basic information

Entry
Database: EMDB / ID: EMD-56097
Titlegp13 protein from vB_PagS_MED16 bacteriophage
Map data
Sample
  • Complex: Major tail protein gp13 from vB_PagS_MED16 bacteriophage
    • Protein or peptide: Major tail protein gp13 from vB_PagS_MED16 bacteriophage
KeywordsvB_PagS_MED16 bacteriophage / bacteriophage tail / VIRAL PROTEIN
Biological speciesPantoea phage vB_PagS_MED16 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSasnauskas G / Tamulaitiene G / Miksys A / Poviloniene S / Casaite V / Meskys R
Funding supportLithuania, 1 items
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, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56097.png

Downloads & links

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Map

FileDownload / File: emd_56097.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.05718897 - 0.36036465
Average (Standard dev.)0.0008114382 (±0.026011374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56097_msk_1.map
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Additional map: Main map sharpened using phenix.auto sharpen 1.21.2-5419 (b iso to d cut procedure)...

Fileemd_56097_additional_1.map
AnnotationMain map sharpened using phenix.auto_sharpen_1.21.2-5419 (b_iso_to_d_cut procedure)
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Half map: #1

Fileemd_56097_half_map_1.map
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Half map: #2

Fileemd_56097_half_map_2.map
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Sample components

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Entire : Major tail protein gp13 from vB_PagS_MED16 bacteriophage

EntireName: Major tail protein gp13 from vB_PagS_MED16 bacteriophage
Components
  • Complex: Major tail protein gp13 from vB_PagS_MED16 bacteriophage
    • Protein or peptide: Major tail protein gp13 from vB_PagS_MED16 bacteriophage

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Supramolecule #1: Major tail protein gp13 from vB_PagS_MED16 bacteriophage

SupramoleculeName: Major tail protein gp13 from vB_PagS_MED16 bacteriophage
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pantoea phage vB_PagS_MED16 (virus)

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Macromolecule #1: Major tail protein gp13 from vB_PagS_MED16 bacteriophage

MacromoleculeName: Major tail protein gp13 from vB_PagS_MED16 bacteriophage
type: protein_or_peptide / ID: 1 / Details: Expression tag at the N-terminus / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Pantoea phage vB_PagS_MED16 (virus)
Molecular weightTheoretical: 28.470914 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAGSHHHHHH GMASMTGGQQ MGRSGWELQM SNYQLPNGSS VQLSTALGDA KDVTGASNAA ECVFTIDNAA GASALAKGDR FILTGSPWI RLSNAVLVVK AATATSVTAL ALDTTDATKY PAGAFSATVK GELRKITNWV DFPYITNVAQ AGGDQQTTSF Q PLQVDEAI ...String:
MAGSHHHHHH GMASMTGGQQ MGRSGWELQM SNYQLPNGSS VQLSTALGDA KDVTGASNAA ECVFTIDNAA GASALAKGDR FILTGSPWI RLSNAVLVVK AATATSVTAL ALDTTDATKY PAGAFSATVK GELRKITNWV DFPYITNVAQ AGGDQQTTSF Q PLQVDEAI QLNTFKNARS VTYTLTHDMD DPVRPILVDG DATQEIHAIQ FINPKARAGK GEIRLYAAKI SFNEVPSAEV NN VETVQAV VSMASTMRFY QKDVVDALK

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 990 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.94 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.75 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 190495
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9to0:
gp13 protein from vB_PagS_MED16 bacteriophage

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