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- PDB-9jhf: Cryo-EM structure of beta-LG fibril -

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Basic information

Entry
Database: PDB / ID: 9jhf
TitleCryo-EM structure of beta-LG fibril
ComponentsBeta-lactoglobulin fibrils
KeywordsPROTEIN FIBRIL / protein fribril / nanomaterials
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsXu, Y.Y. / Liu, C.
Funding support1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Beta-lactoglobulin fibrils
AB: Beta-lactoglobulin fibrils
AC: Beta-lactoglobulin fibrils
AE: Beta-lactoglobulin fibrils
AD: Beta-lactoglobulin fibrils
AF: Beta-lactoglobulin fibrils


Theoretical massNumber of molelcules
Total (without water)20,6466
Polymers20,6466
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Beta-lactoglobulin fibrils / Beta-LG


Mass: 3441.067 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
Has protein modificationN

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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: Beta-Lactoglobulin fibril in Bos taurus whey / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 2
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: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13Coot3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -2.38 ° / Axial rise/subunit: 4.81 Å / Axial symmetry: C1
3D reconstructionResolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31562 / Symmetry type: HELICAL

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