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- PDB-10sd: The cryoEM structure of T10 type2 nanofiber -

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Basic information

Entry
Database: PDB / ID: 10sd
TitleThe cryoEM structure of T10 type2 nanofiber
ComponentsT10 type 2 nanofiber
KeywordsPROTEIN FIBRIL / nanofiber
Function / homologyDECANOIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.11 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
B: T10 type 2 nanofiber
C: T10 type 2 nanofiber
D: T10 type 2 nanofiber
E: T10 type 2 nanofiber
F: T10 type 2 nanofiber
G: T10 type 2 nanofiber
H: T10 type 2 nanofiber
I: T10 type 2 nanofiber
J: T10 type 2 nanofiber
K: T10 type 2 nanofiber
L: T10 type 2 nanofiber
M: T10 type 2 nanofiber
O: T10 type 2 nanofiber
P: T10 type 2 nanofiber
Q: T10 type 2 nanofiber
A: T10 type 2 nanofiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,88032
Polymers17,12416
Non-polymers2,75616
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.99965, -0.026456), (0.026456, 0.99965), (1)3.71, -3.6131, -9.6
3generate(0.999913, -0.013229), (0.013229, 0.999913), (1)1.843, -1.8188, -4.8
4generate(0.999913, 0.013229), (-0.013229, 0.999913), (1)-1.8188, 1.843, 4.8
5generate(0.99965, 0.026456), (-0.026456, 0.99965), (1)-3.6131, 3.71, 9.6
6generate(0.999213, 0.039678), (-0.039678, 0.999213), (1)-5.3825, 5.6005, 14.4

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Components

#1: Protein/peptide
T10 type 2 nanofiber


Mass: 1070.266 Da / Num. of mol.: 16 / Source method: obtained synthetically / Details: HYPIVIGGSK(NH2) / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H20O2 / 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: T10 type2 / Type: COMPLEX / Entity ID: #1 / Source: SYNTHETIC
Molecular weightValue: 1.915 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

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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2REFMAC5.8.0430model refinement
13Servalcat3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -0.758 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37 / Symmetry type: HELICAL
RefinementResolution: 3.11→115.91 Å / Cor.coef. Fo:Fc: 0.748 / SU B: 25.262 / SU ML: 0.433 / ESU R: 0.236
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.48104 --
obs0.48104 60900 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 111.112 Å2
Refinement stepCycle: 1 / Total: 1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0121405
ELECTRON MICROSCOPYr_bond_other_d0.0010.0161418
ELECTRON MICROSCOPYr_angle_refined_deg1.7411.8161853
ELECTRON MICROSCOPYr_angle_other_deg0.8541.6823345
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.0615144
ELECTRON MICROSCOPYr_dihedral_angle_2_deg8.959516
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.5410192
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0670.2176
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.021424
ELECTRON MICROSCOPYr_gen_planes_other0.0050.02240
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it13.2489.184624
ELECTRON MICROSCOPYr_mcbond_other13.2489.185624
ELECTRON MICROSCOPYr_mcangle_it23.28916.294752
ELECTRON MICROSCOPYr_mcangle_other23.27416.286753
ELECTRON MICROSCOPYr_scbond_it11.08314.091781
ELECTRON MICROSCOPYr_scbond_other11.07614.084782
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other20.7824.841102
ELECTRON MICROSCOPYr_long_range_B_refined35.801124.011274
ELECTRON MICROSCOPYr_long_range_B_other35.792123.991275
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.11→3.191 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.939 4509 -
obs--100 %

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