10SE | pdb_000010se

The CryoEM structure of T8 nanofiber


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 10SE

This is version 1.0 of the entry. See complete history

Literature

Tailoring Avidity through Morphology: Structure-Avidity Relationship in CD38-Binding Nanofiber Radiotracers.

Godbe, J.M.Zhang, H.Sharma, A.K.Ernst, K.N.Jing, Z.Dyer, M.R.Prior, J.L.Teubner, E.Manion, B.Tang, R.Yang, Y.Shokeen, M.

(2026) ACS Appl Bio Mater 9: 4242-4257

  • DOI: https://doi.org/10.1021/acsabm.6c00348
  • Primary Citation Related Structures: 
    10SD, 10SE, 10SF, 10SG, 10SH

  • PubMed Abstract: 

    The lack of targeted molecular imaging agents for multiple myeloma (MM) hinders precise disease characterization and theranostic development. We address this by engineering a tunable platform of self-assembled peptide nanofibers that target CD38, a key antigen in MM. Simple variation of a conjugated lipid tail length (C4-C12) dictates the supramolecular architecture, as revealed by high-resolution cryo-EM. This structural control directly modulates biological function: avidity for CD38 increases monotonically with tail length, culminating in T12 nanofibers with sub-nanomolar affinity. This optimized morphology also enables unique pH-responsive di-tyrosine cross-linking and, critically, facilitates polyvalent cell-surface engagement that outcompetes high-affinity monomers in vitro. The nanofibers are efficiently radiolabeled with 64 Cu, exhibit exceptional serum stability, and show no toxicity at doses 20-fold above projected imaging use. By establishing lipid tail length as a simple, powerful handle for controlling nanofiber structure, avidity, and function, we present a robust, translatable platform for advancing targeted imaging and therapy in CD38-positive malignancies.


  • Organizational Affiliation
    • Edward Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States.

Macromolecule Content 

  • Total Structure Weight: 21.86 kDa 
  • Atom Count: 1,530 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

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Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OCA

Query on OCA



Download:Ideal Coordinates CCD File
AA [auth I]
BA [auth K]
CA [auth L]
DA [auth M]
EA [auth N]
AA [auth I],
BA [auth K],
CA [auth L],
DA [auth M],
EA [auth N],
FA [auth P],
GA [auth Q],
HA [auth R],
IA [auth O],
JA [auth J],
S [auth E],
T [auth A],
U [auth B],
V [auth C],
W [auth D],
X [auth F],
Y [auth G],
Z [auth H]
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0430
RECONSTRUCTIONServalcat

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release