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- PDB-11ok: Phage Tail Tube Protein from ALys extract -

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Basic information

Entry
Database: PDB / ID: 11ok
TitlePhage Tail Tube Protein from ALys extract
ComponentsPhage tail tube protein
KeywordsVIRAL PROTEIN / Helical assembly / phage tail tube protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSchaefer, J.H. / Lander, G.C.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095892 United States
German Research Foundation (DFG)556478029 Germany
CitationJournal: Biorxiv / Year: 2026
Title: Siphoviridae phage tails co-enrich with ex vivo amyloids
Authors: Schafer, J.H. / O'Neill, R.T. / Grotjahn, D. / Powers, E.T. / Kelly, J.W. / Lander, G.C.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)207,34112
Polymers207,34112
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

#1: Protein
Phage tail tube protein


Mass: 17278.418 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / References: UniProt: D9SPF2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Phage tail tube protein / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bacteriophage sp. (virus)
Details of virusEmpty: YES / Isolate: OTHER
Buffer solutionpH: 7
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: 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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49.36 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 14.17 ° / Axial rise/subunit: 37.23 Å / Axial symmetry: C6
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21244 / Symmetry type: HELICAL
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314208
ELECTRON MICROSCOPYf_angle_d0.7519188
ELECTRON MICROSCOPYf_dihedral_angle_d5.8431956
ELECTRON MICROSCOPYf_chiral_restr0.0462220
ELECTRON MICROSCOPYf_plane_restr0.0032460

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