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- PDB-9vnk: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph2 -

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Basic information

Entry
Database: PDB / ID: 9vnk
TitleCryo-EM structure of hnRAC1-2,8beta fibril polymorph2
ComponentsGLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
KeywordsPROTEIN FIBRIL / beta amino acid modified peptide
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsLi, Y.S. / Li, D.N. / Dai, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nano Lett / Year: 2025
Title: Conformational Adaptability and Thermostability in α/β-Peptide Fibrils Induced by β-Amino Acid Substitution.
Authors: Yingshan Li / Danni Li / Yuxuan Yao / Kaien Liu / Qinyue Zhao / Yiling Zhang / Yongyi Xu / Dan Li / Bo Sun / Cong Liu / Bin Dai /
Abstract: The self-assembly of peptides into amyloid fibrils enables the design of functional biomaterials, yet the conformational constraints of α-peptides limit the attainable supramolecular diversity. ...The self-assembly of peptides into amyloid fibrils enables the design of functional biomaterials, yet the conformational constraints of α-peptides limit the attainable supramolecular diversity. Here, we introduce β-amino acids, β-phenylalanine (β-Phe), and β-homophenylalanine (β-hPhe) into the reversible fibril-forming core sequence hnRAC1 to generate α/β-peptide variants with distinct architectures and enhanced thermal stability. Cryo-EM reveals that β-modified peptides assemble into polymorphic fibrils with cross-β structures that differ markedly from each other and from native hnRAC1. Comparative structural analysis indicates that backbone extension by β-residues increases subunit conformational heterogeneity, enabling tighter packing and formation of more thermostable fibrils. Examination of intra- and intermolecular contacts shows that enhanced π-π stacking, hydrophobic interactions, hydrogen bonds, and electrostatic interactions likely contribute to fibril stabilization. These results show that minimal backbone modifications can remodel amyloid architecture, offering a generalizable strategy for designing structurally diverse and robust peptide-based biomaterials.
History
DepositionJun 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data 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
A: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
D: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
H: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
I: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
L: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
O: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
Q: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
B: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
G: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
C: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
F: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
K: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
M: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
N: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
P: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
R: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
E: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
J: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
S: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
Y: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
g: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
i: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
o: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
u: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
y: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
U: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
e: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
W: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
c: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
m: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
q: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
s: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
w: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
0: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
a: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
k: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
T: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
Z: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
h: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
j: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
p: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
v: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
z: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
V: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
f: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
X: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
d: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
n: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
r: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
t: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
x: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
1: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
b: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
l: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY


Theoretical massNumber of molelcules
Total (without water)47,72954
Polymers47,72954
Non-polymers00
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 ...
GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY


Mass: 883.863 Da / Num. of mol.: 54 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY
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: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
9PHENIX1.20.1-4487model refinement
13RELION33D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -0.96 ° / Axial rise/subunit: 4.81 Å / Axial symmetry: C1
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8973 / Symmetry type: HELICAL

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