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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: To Be Published
Title: Structural Insights and Functional Dynamics of Beta-Lactoglobulin Fibrils
Authors: Sternke-Hoffmann, R. / Rhyner, D. / Juranyi, F. / Qureshi, B. / Riek, R. / Greenwald, J. / Luetz-Bueno, V. / Luo, J.
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

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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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