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- EMDB-65213: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1 -

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Basic information

Entry
Database: EMDB / ID: EMD-65213
TitleCryo-EM structure of hnRAC1-2,8beta fibril polymorph1
Map data
Sample
  • Complex: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1
    • Protein or peptide: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY
Keywordsbeta amino acid modified peptide / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsLi YS / Li DN / Dai B
Funding support1 items
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, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65213.png

Downloads & links

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Map

FileDownload / File: emd_65213.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0122
Minimum - Maximum-0.025783028 - 0.049867388
Average (Standard dev.)0.00028323176 (±0.0023120793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65213_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65213_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1

EntireName: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1
Components
  • Complex: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1
    • Protein or peptide: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY

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Supramolecule #1: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1

SupramoleculeName: Cryo-EM structure of hnRAC1-2,8beta fibril polymorph1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY

MacromoleculeName: GLY-SFE-GLY-GLY-ASN-ASP-ASN-SFE-GLY / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 883.863 Da
SequenceString:
G(SFE)GGNDN(SFE)G

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.79 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.28 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 7412
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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