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- EMDB-52781: Structure of beta-lactoglobulin fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-52781
TitleStructure of beta-lactoglobulin fibril
Map data
Sample
  • Complex: Beta-lactoglobulin fibril
    • Protein or peptide: Beta-lactoglobulin
KeywordsWhey protein / Nutrient transport / Amyloid fibrillation / Cross-beta structure / Nanomaterial / BIOSYNTHETIC PROTEIN
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: 3.17 Å
AuthorsSternke-Hoffmann R / Rhyner D / Qureshi B / Riek R / Greenwald J / Luo J
Funding support Switzerland, 2 items
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, 2025-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52781.png

Downloads & links

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Map

FileDownload / File: emd_52781.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.08999902 - 0.17101784
Average (Standard dev.)0.000105352614 (±0.004884785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52781_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52781_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52781_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Beta-lactoglobulin fibril

EntireName: Beta-lactoglobulin fibril
Components
  • Complex: Beta-lactoglobulin fibril
    • Protein or peptide: Beta-lactoglobulin

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Supramolecule #1: Beta-lactoglobulin fibril

SupramoleculeName: Beta-lactoglobulin fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Beta-lactoglobulin

MacromoleculeName: Beta-lactoglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 3.627232 KDa
SequenceString:
LIVTQTMKGL DIQKVAGTWY SLAMAASDIS LLDA

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

Concentration7 mg/mL
BufferpH: 2.5 / Component - Concentration: 25.0 mM / Component - Name: Citric acid-sodium phosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa
Details: PELCO easiGLOW Glow discharge cleaning system using 25 mA for 30 s.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3.7 ul sample was applied and blotted for 6 s after a wait time of 30 s with a force of 0.
DetailsThis sample was monodisperse. The sample was prepared at 7 mg/ml and diluted 15 times for EM grid.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 88.15 K / Max: 93.15 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 16475 / Average exposure time: 1.0 sec. / Average electron dose: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.80359 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.73567 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 67843
Segment selectionNumber selected: 1387479
Details: from 3825 micrographs selected based on rlnCtfMaxResolution with a cut-off of 4 A
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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