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- EMDB-75434: The CryoEM structure of T12 type1 nanofiber -

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Basic information

Entry
Database: EMDB / ID: EMD-75434
TitleThe CryoEM structure of T12 type1 nanofiber
Map data
Sample
  • Complex: T12 type1 nanofiber
    • Protein or peptide: T12 type 1 nanofiber
  • Ligand: LAURIC ACID
Keywordsnanofiber / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsZhang H / Yang Y
Funding support1 items
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, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75434.png

Downloads & links

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Map

FileDownload / File: emd_75434.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 256 pix.
= 198.656 Å		0.78 Å/pix.
x 256 pix.
= 198.656 Å		0.78 Å/pix.
x 256 pix.
= 198.656 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.776 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0064
Minimum - Maximum-0.015894473 - 0.034684464
Average (Standard dev.)0.00023292744 (±0.0013817874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 198.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75434_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75434_half_map_2.map
Projections & Slices
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Sample components

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Entire : T12 type1 nanofiber

EntireName: T12 type1 nanofiber
Components
  • Complex: T12 type1 nanofiber
    • Protein or peptide: T12 type 1 nanofiber
  • Ligand: LAURIC ACID

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Supramolecule #1: T12 type1 nanofiber

SupramoleculeName: T12 type1 nanofiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes
Molecular weightTheoretical: 1.943 kDa/nm

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Macromolecule #1: T12 type 1 nanofiber

MacromoleculeName: T12 type 1 nanofiber / type: protein_or_peptide / ID: 1 / Details: HYPIVIGGSK(NH2) / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.070266 KDa
SequenceString:
HYPIVIGGSK (NH2)

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Macromolecule #2: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 2 / Number of copies: 12 / Formula: DAO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.77 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.695 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Servalcat / Number images used: 35
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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