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- EMDB-61481: Cryo-em structure of beta-LG fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-61481
TitleCryo-em structure of beta-LG fibril
Map data
Sample
  • Organelle or cellular component: Beta-Lactoglobulin fibril in Bos taurus whey
    • Protein or peptide: Beta-lactoglobulin fibrils
Keywordsprotein fribril / nanomaterials / PROTEIN FIBRIL
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
Methodhelical reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsXu YY / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nano Lett / Year: 2025
Title: β-Lactoglobulin Forms a Conserved Fibril Core That Assembles into Diverse Fibril Polymorphs.
Authors: Yongyi Xu / Danni Li / Yiling Zhang / Qinyue Zhao / Bo Sun / Cong Liu / Dan Li / Bin Dai /
Abstract: The β-lactoglobulin (β-LG) protein, sourced from dietary products, is notable for forming amyloid fibrils, which are increasingly recognized as valuable protein-based nanomaterials due to their ...The β-lactoglobulin (β-LG) protein, sourced from dietary products, is notable for forming amyloid fibrils, which are increasingly recognized as valuable protein-based nanomaterials due to their superior cytocompatibility, chemical resilience, and mechanical characteristics. However, the precise atomic details of β-LG's fibril assembly are not understood. In this study, we utilized cryo-electron microscopy to elucidate the composition and architecture of β-LG fibrils. We discovered that the β-LG fibril was rapidly assembled after a short time incubation. Remarkably, these fibril cores were composed of the first 32 residues, forming four β-strands that adopted a serpentine arrangement into a single protofilament. This protofilament core's stability was reinforced by hydrophobic interactions. Two identical protofilaments then align to form four distinct structural polymorphs through unique interfacial configurations, which were stabilized by hydrophilic interactions, hydrogen bonding, and electrostatic forces. Our findings provide a structural framework for understanding β-LG fibril formation and pave the way for designing innovative β-LG-based nanomaterials.
History
DepositionSep 9, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61481.png

Downloads & links

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Map

FileDownload / File: emd_61481.map.gz / Format: CCP4 / Size: 40.6 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 220 pix.
= 182.6 Å		0.83 Å/pix.
x 220 pix.
= 182.6 Å		0.83 Å/pix.
x 220 pix.
= 182.6 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: 0.001
Minimum - Maximum-0.036073834 - 0.05897881
Average (Standard dev.)0.00024583342 (±0.0024501963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 182.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61481_msk_1.map
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Half map: #2

Fileemd_61481_half_map_1.map
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Half map: #1

Fileemd_61481_half_map_2.map
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Sample components

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Entire : Beta-Lactoglobulin fibril in Bos taurus whey

EntireName: Beta-Lactoglobulin fibril in Bos taurus whey
Components
  • Organelle or cellular component: Beta-Lactoglobulin fibril in Bos taurus whey
    • Protein or peptide: Beta-lactoglobulin fibrils

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Supramolecule #1: Beta-Lactoglobulin fibril in Bos taurus whey

SupramoleculeName: Beta-Lactoglobulin fibril in Bos taurus whey / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Beta-lactoglobulin fibrils

MacromoleculeName: Beta-lactoglobulin fibrils / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 3.441067 KDa
SequenceString:
LIVTQTMKGL DIQKVAGTWY SLAMAASDIS LL

UniProtKB: Beta-lactoglobulin

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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: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 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: -2.49 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 38795
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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