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- EMDB-61056: Cryo-EM Structure of Lysozyme Type 1 Amyloid Fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-61056
TitleCryo-EM Structure of Lysozyme Type 1 Amyloid Fibrils
Map datafullmap
Sample
  • Complex: Hen egg white lysozyme (HEWL) amyloid
    • Protein or peptide: Lysozyme C
  • Ligand: water
Keywordsamyloid / fibril / lysozyme / hen egg white lysozyme / HEWL / PROTEIN FIBRIL
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsKawabata H / Park SY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for amyloid fibril formation by lysozyme
Authors: Kawabata H / Li Y / Lin Y / Ishimoto N / Yun Y / Heo Y / Park JH / Lee YH / Park SY
History
DepositionAug 2, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61056.png

Downloads & links

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Map

FileDownload / File: emd_61056.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfullmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 279.441 Å		0.73 Å/pix.
x 384 pix.
= 279.441 Å		0.73 Å/pix.
x 384 pix.
= 279.441 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72771 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00197
Minimum - Maximum-0.013731868 - 0.027151866
Average (Standard dev.)-0.0000014730269 (±0.0013000522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.44104 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61056_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: postprocess sharpened map

Fileemd_61056_additional_1.map
Annotationpostprocess sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2

Fileemd_61056_half_map_1.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_61056_half_map_2.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hen egg white lysozyme (HEWL) amyloid

EntireName: Hen egg white lysozyme (HEWL) amyloid
Components
  • Complex: Hen egg white lysozyme (HEWL) amyloid
    • Protein or peptide: Lysozyme C
  • Ligand: water

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Supramolecule #1: Hen egg white lysozyme (HEWL) amyloid

SupramoleculeName: Hen egg white lysozyme (HEWL) amyloid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Lysozyme C

MacromoleculeName: Lysozyme C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 13.898624 KDa
SequenceString:
RCELAAAMKR HGLDNYRGYS LGNWVCAAKF ESNFNTQATN RNTDGSTDYG ILQINSRWWC NDGRTPGSRN LCNIPCSALL SSDITASVN CAKKIVSDGN GMNAWVAWRN RCKGTDVQAW IRGCRL

UniProtKB: Lysozyme C

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 17 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration5 mg/mL
BufferpH: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.38573 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.79 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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