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- PDB-10sg: The CryoEM structure of T12 type1 nanofiber -

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Basic information

Entry
Database: PDB / ID: 10sg
TitleThe CryoEM structure of T12 type1 nanofiber
ComponentsT12 type 1 nanofiber
KeywordsPROTEIN FIBRIL / nanofiber
Function / homologyLAURIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsZhang, H. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: ACS Appl Bio Mater / Year: 2026
Title: Tailoring Avidity through Morphology: Structure-Avidity Relationship in CD38-Binding Nanofiber Radiotracers.
Authors: Jacqueline M Godbe / Hongwei Zhang / Amit K Sharma / Katelyn N Ernst / Zhenghan Jing / Michael R Dyer / Julie L Prior / Erin Teubner / Brad Manion / Rui Tang / Yang Yang / Monica Shokeen /
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- ...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 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.
History
DepositionFeb 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T12 type 1 nanofiber
B: T12 type 1 nanofiber
C: T12 type 1 nanofiber
D: T12 type 1 nanofiber
E: T12 type 1 nanofiber
F: T12 type 1 nanofiber
G: T12 type 1 nanofiber
H: T12 type 1 nanofiber
I: T12 type 1 nanofiber
J: T12 type 1 nanofiber
K: T12 type 1 nanofiber
L: T12 type 1 nanofiber
M: T12 type 1 nanofiber
N: T12 type 1 nanofiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,38826
Polymers14,98414
Non-polymers2,40412
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
T12 type 1 nanofiber


Mass: 1070.266 Da / Num. of mol.: 14 / Source method: obtained synthetically / Details: HYPIVIGGSK(NH2) / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H24O2 / Source: (synth.) synthetic construct (others)
Has ligand of interestN
Has protein modificationY

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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: T12 type1 nanofiber / Type: COMPLEX / Entity ID: #1 / Source: SYNTHETIC
Molecular weightValue: 1.943 kDa/nm / Experimental value: YES
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13Servalcat3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -0.695 ° / Axial rise/subunit: 4.77 Å / Axial symmetry: C1
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35 / Symmetry type: HELICAL

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