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- PDB-10sf: The CryoEM structure of T10 type1 nanofiber -

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Basic information

Entry
Database: PDB / ID: 10sf
TitleThe CryoEM structure of T10 type1 nanofiber
ComponentsType10 type 1 nanofiber
KeywordsPROTEIN FIBRIL / nanofiber
Function / homologyDECANOIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.08 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 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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

Downloads & links

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Assembly

Deposited unit
E: Type10 type 1 nanofiber
A: Type10 type 1 nanofiber
B: Type10 type 1 nanofiber
C: Type10 type 1 nanofiber
D: Type10 type 1 nanofiber
F: Type10 type 1 nanofiber
G: Type10 type 1 nanofiber
H: Type10 type 1 nanofiber
I: Type10 type 1 nanofiber
J: Type10 type 1 nanofiber
K: Type10 type 1 nanofiber
L: Type10 type 1 nanofiber
M: Type10 type 1 nanofiber
N: Type10 type 1 nanofiber
O: Type10 type 1 nanofiber
P: Type10 type 1 nanofiber
Q: Type10 type 1 nanofiber
R: Type10 type 1 nanofiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,36636
Polymers19,26518
Non-polymers3,10118
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(0.998813, -0.04871), (0.04871, 0.998813), (1)6.9058, -6.5772, -19.16
3generate(0.999332, -0.036539), (0.036539, 0.999332), (1)5.1494, -4.9646, -14.37
4generate(0.999703, -0.024362), (0.024362, 0.999703), (1)3.4128, -3.3307, -9.58
5generate(0.999926, -0.012182), (0.012182, 0.999926), (1)1.6963, -1.6757, -4.79
6generate(0.999926, 0.012182), (-0.012182, 0.999926), (1)-1.6757, 1.6963, 4.79
7generate(0.999703, 0.024362), (-0.024362, 0.999703), (1)-3.3307, 3.4128, 9.58
8generate(0.999332, 0.036539), (-0.036539, 0.999332), (1)-4.9646, 5.1494, 14.37

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Components

#1: Protein/peptide
Type10 type 1 nanofiber


Mass: 1070.266 Da / Num. of mol.: 18 / 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.: 18 / 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 type1 nanofiber / Type: COMPLEX / Entity ID: #1 / Source: SYNTHETIC
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: -0.698 ° / Axial rise/subunit: 4.79 Å / Axial symmetry: C1
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35 / Symmetry type: HELICAL
RefinementResolution: 3.08→3.08 Å / Cor.coef. Fo:Fc: 0.706 / SU B: 20.442 / SU ML: 0.358 / ESU R: 0.211
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.46279 --
obs0.46279 78996 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 113.103 Å2
Refinement stepCycle: 1 / Total: 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0121602
ELECTRON MICROSCOPYr_bond_other_d0.0010.0161638
ELECTRON MICROSCOPYr_angle_refined_deg1.6951.8262106
ELECTRON MICROSCOPYr_angle_other_deg0.8281.6783870
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.65162
ELECTRON MICROSCOPYr_dihedral_angle_2_deg10.679518
ELECTRON MICROSCOPYr_dihedral_angle_3_deg8.07410216
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0510.2198
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.021602
ELECTRON MICROSCOPYr_gen_planes_other0.0040.02270
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_it12.8599.238702
ELECTRON MICROSCOPYr_mcbond_other12.859.234703
ELECTRON MICROSCOPYr_mcangle_it21.23216.458846
ELECTRON MICROSCOPYr_mcangle_other21.2216.451847
ELECTRON MICROSCOPYr_scbond_it11.60414.117900
ELECTRON MICROSCOPYr_scbond_other11.59814.111901
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other21.18324.7691261
ELECTRON MICROSCOPYr_long_range_B_refined33.435122.151436
ELECTRON MICROSCOPYr_long_range_B_other33.424122.121437
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.956 5805 -
obs--100 %

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