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- PDB-10sh: The CryoEM structure of T12 type2 nanofiber -

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Basic information

Entry
Database: PDB / ID: 10sh
TitleThe CryoEM structure of T12 type2 nanofiber
ComponentsT12 type 2 nanofiber
KeywordsPROTEIN FIBRIL / nanofiber
Function / homologyLAURIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhang, H. / Yang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
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

Downloads & links

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Assembly

Deposited unit
D: T12 type 2 nanofiber
H: T12 type 2 nanofiber
J: T12 type 2 nanofiber
K: T12 type 2 nanofiber
L: T12 type 2 nanofiber
O: T12 type 2 nanofiber
P: T12 type 2 nanofiber
R: T12 type 2 nanofiber
S: T12 type 2 nanofiber
T: T12 type 2 nanofiber
Y: T12 type 2 nanofiber
Z: T12 type 2 nanofiber
8: T12 type 2 nanofiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,51826
Polymers13,91313
Non-polymers2,60413
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(0.999334, -0.036487), (0.036487, 0.999334), (1)3.6903, -3.558, -14.25
3generate(0.999704, -0.024327), (0.024327, 0.999704), (1)2.4458, -2.387, -9.5
4generate(0.999926, -0.012165), (0.012165, 0.999926), (1)1.2156, -1.2009, -4.75
5generate(0.999926, 0.012165), (-0.012165, 0.999926), (1)-1.2009, 1.2156, 4.75
6generate(0.999704, 0.024327), (-0.024327, 0.999704), (1)-2.387, 2.4458, 9.5

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Components

#1: Protein/peptide
T12 type 2 nanofiber


Mass: 1070.266 Da / Num. of mol.: 13 / 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.: 13 / 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 type2 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
IDNameVersionCategory
1RELIONparticle selection
2REFMAC5.8.0430model refinement
13Servalcat3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -0.697 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C1
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35 / Symmetry type: HELICAL
RefinementResolution: 2.97→2.97 Å / Cor.coef. Fo:Fc: 0.891 / SU B: 14.262 / SU ML: 0.267 / ESU R: 0.172
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.38893 --
obs0.38893 56425 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 128.111 Å2
Refinement stepCycle: 1 / Total: 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.0121183
ELECTRON MICROSCOPYr_bond_other_d0.0010.0161235
ELECTRON MICROSCOPYr_angle_refined_deg1.7171.8461547
ELECTRON MICROSCOPYr_angle_other_deg0.7881.6732925
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.6125117
ELECTRON MICROSCOPYr_dihedral_angle_2_deg11.126513
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.51910156
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0770.2143
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.021157
ELECTRON MICROSCOPYr_gen_planes_other0.0040.02195
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_it18.65611.768507
ELECTRON MICROSCOPYr_mcbond_other18.64311.761507
ELECTRON MICROSCOPYr_mcangle_it29.22621.151611
ELECTRON MICROSCOPYr_mcangle_other29.22121.155612
ELECTRON MICROSCOPYr_scbond_it15.28715.382676
ELECTRON MICROSCOPYr_scbond_other15.27715.378677
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other25.45928.07937
ELECTRON MICROSCOPYr_long_range_B_refined42.568153.371016
ELECTRON MICROSCOPYr_long_range_B_other42.548153.331017
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.96→3.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.88 4074 -
obs--100 %

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