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- EMDB-56098: gp39 protein from Escherichia phage vB_EcoS_NBD2 -

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Basic information

Entry
Database: EMDB / ID: EMD-56098
Titlegp39 protein from Escherichia phage vB_EcoS_NBD2
Map data
Sample
  • Complex: Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2
    • Protein or peptide: Putative major tail protein
KeywordsvB_EcoS_NBD2 bacteriophage / bacteriophage tail / VIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSasnauskas G / Tamulaitiene G / 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_56098.png

Downloads & links

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Map

FileDownload / File: emd_56098.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.16719474 - 0.37039766
Average (Standard dev.)0.002987616 (±0.021503864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56098_msk_1.map
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Additional map: Main map sharpened using phenix.auto sharpen 1.21.2-5419 and b iso to c cut function...

Fileemd_56098_additional_1.map
AnnotationMain map sharpened using phenix.auto_sharpen_1.21.2-5419 and b_iso_to_c_cut function
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Half map: #2

Fileemd_56098_half_map_1.map
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Half map: #1

Fileemd_56098_half_map_2.map
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Sample components

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Entire : Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2

EntireName: Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2
Components
  • Complex: Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2
    • Protein or peptide: Putative major tail protein

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Supramolecule #1: Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2

SupramoleculeName: Major tail protein gp39 from Escherichia phage vB_EcoS_NBD2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage vB_EcoS_NBD2 (virus)

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Macromolecule #1: Putative major tail protein

MacromoleculeName: Putative major tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoS_NBD2 (virus)
Molecular weightTheoretical: 24.380301 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSLPNGSKVF IERTRAAQEI TASAISNAEN PVATVNSTTG LAVGDFVLVT ESVWAGLKNR VLRIKTVTAD TSITLEGDKS TSTVNLNKY PAGGASTLVK ITSWIEIPCV SDIAKSGGEQ QYYTKQCLSD DRERQIPTFK SATSIAYTFD FDYANPVTDL L IGYDEDGK ...String:
MSLPNGSKVF IERTRAAQEI TASAISNAEN PVATVNSTTG LAVGDFVLVT ESVWAGLKNR VLRIKTVTAD TSITLEGDKS TSTVNLNKY PAGGASTLVK ITSWIEIPCV SDIAKSGGEQ QYYTKQCLSD DRERQIPTFK SATSIAYTFD FDYANPVTDL L IGYDEDGK TRALYMFVPK ASFPIRAFSG VPSFDDVPNT VMNEDETTIL TISLDGKYVH MQGEVD

UniProtKB: Putative major tail protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
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: 890 / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 54474
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.7)
Output model

PDB-9toi:
gp39 protein from Escherichia phage vB_EcoS_NBD2

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