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- PDB-9iah: Structure of beta-lactoglobulin fibril -

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Basic information

Entry
Database: PDB / ID: 9iah
TitleStructure of beta-lactoglobulin fibril
ComponentsBeta-lactoglobulin
KeywordsBIOSYNTHETIC PROTEIN / Whey protein / Nutrient transport / Amyloid fibrillation / Cross-beta structure / Nanomaterial
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: 3.17 Å
AuthorsSternke-Hoffmann, R. / Rhyner, D. / Qureshi, B. / Riek, R. / Greenwald, J. / Luo, J.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation10002967 Switzerland
Swiss National Science Foundation197626 Switzerland
CitationJournal: Nano Lett / Year: 2025
Title: Structural Insights and Functional Dynamics of β-Lactoglobulin Fibrils.
Authors: Rebecca Sternke-Hoffmann / David Rhyner / Genki Terashi / Bilal Muhammad Qureshi / Roland Riek / Jason Greenwald / Daisuke Kihara / Viviane Lutz-Bueno / Jinghui Luo /
Abstract: Amyloid fibrils from β-lactoglobulin (β-LG), a major whey protein, have attracted interest for nanotechnology due to their biocompatibility, tunable surface chemistry, and ability to bind ...Amyloid fibrils from β-lactoglobulin (β-LG), a major whey protein, have attracted interest for nanotechnology due to their biocompatibility, tunable surface chemistry, and ability to bind functional molecules. They serve as scaffolds for metal nanoparticle synthesis, carriers for bioactive compounds, and building blocks for nanomaterials with tailored mechanical and optical properties. However, their dynamic architecture remains incompletely understood, limiting their rational design. Here, we combine cryo-electron microscopy (cryo-EM), small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations to investigate β-LG fibrils formed under mildly denaturing conditions. Cryo-EM reveals a monomeric polymorph with a conserved core (Leu1-Ala34) and a disordered "fuzzy coat". Flexible domains were modeled and evaluated by MD, identifying one stable conformation (Asn90-Thr97). The ionic strength reduced the coat flexibility and promoted iron binding, suggesting environmental responsiveness. These findings link fibril flexibility to functional potential, offering mechanistic insight into engineering β-LG-based nanomaterials.
History
DepositionFeb 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Beta-lactoglobulin
D: Beta-lactoglobulin
C: Beta-lactoglobulin
B: Beta-lactoglobulin
A: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)18,1365
Polymers18,1365
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
Beta-lactoglobulin / Beta-LG


Mass: 3627.232 Da / Num. of mol.: 5 / 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 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 2.5
Buffer componentConc.: 25 mM / Name: Citric acid-sodium phosphate
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was monodisperse. The sample was prepared at 7 mg/ml and diluted 15 times for EM grid.
Specimen supportDetails: PELCO easiGLOW Glow discharge cleaning system using 25 mA for 30 s.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 295.15 K
Details: 3.7 ul sample was applied and blotted for 6 s after a wait time of 30 s with a force of 0

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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 magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93.15 K / Temperature (min): 88.15 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 57.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 16475
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
2EPU3.2.0.4776image acquisition
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11-2.73764.80371C1
21-2.735674.80359C1
Particle selectionNum. of particles selected: 1387479
Details: from 3825 micrographs selected based on rlnCtfMaxResolution with a cut-off of 4 A
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67843 / Symmetry type: HELICAL

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