[English] 日本語
Yorodumi
- EMDB-52781: Structure of beta-lactoglobulin fibril -

+
Open data


ID or keywords:

Loading...

-
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: 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, 2025-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52781.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_52781_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52781_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52781_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Beta-lactoglobulin fibril

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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
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.

-
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

+
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more