11OK | pdb_000011ok

Phage Tail Tube Protein from ALys extract

  • Classification: VIRAL PROTEIN
  • Organism(s): Bacteriophage sp.
  • Mutation(s): No 

  • Deposited: 2026-03-06 Released: 2026-07-01 
  • Deposition Author(s): Schaefer, J.H., Lander, G.C.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 11OK

This is version 1.1 of the entry. See complete history

Literature

Siphoviridae phage tails co-enrich with ex vivo amyloids.

Schafer, J.H.O'Neill, R.T.Grotjahn, D.Powers, E.T.Kelly, J.W.Lander, G.C.

(2026) bioRxiv 

  • DOI: https://doi.org/10.64898/2026.06.17.733002
  • Primary Citation Related Structures: 
    11OK

  • PubMed Abstract: 

    Bacteriophages are ubiquitous in the environment and are part of the natural human microbiome. Despite their abundance, the role of the human phagome in health and disease remains poorly understood. Here, we identify phage tails in ex vivo amyloid extracts from patients with lysozyme amyloidosis (ALys) and light-chain amyloidosis (AL). Using cryo-EM analysis of the ALys dataset, automated model building, and database searches, we assigned the observed tubular assemblies to a phage tail tube protein (TTP). Although we cannot fully rule out the possibility of contamination, the presence of phage tails raises the question of whether they bind to and are co-purified with amyloid fibrils. These structures may provide further insight into the potential relationship between phage-derived assemblies and amyloid remodeling, with possible implications for future therapeutic strategies in human amyloidosis.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 207.34 kDa 
  • Atom Count: 14,004 
  • Modeled Residue Count: 1,848 
  • Deposited Residue Count: 1,920 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage tail tube protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
160Bacteriophage sp.Mutation(s): 0 
UniProt
Find proteins for D9SPF2 (Clostridium cellulovorans (strain ATCC 35296 / DSM 3052 / OCM 3 / 743B))
Explore D9SPF2 
Go to UniProtKB:  D9SPF2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9SPF2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095892
German Research Foundation (DFG)Germany556478029

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Database references