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- PDB-9j0m: Cryo-EM Structure of Lysozyme Type 2 Amyloid Fibrils -

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Basic information

Entry
Database: PDB / ID: 9j0m
TitleCryo-EM Structure of Lysozyme Type 2 Amyloid Fibrils
ComponentsLysozyme C
KeywordsPROTEIN FIBRIL / amyloid / fibril / lysozyme / hen egg white lysozyme / HEWL
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsKawabata, H. / Park, S.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for amyloid fibril formation by lysozyme
Authors: Kawabata, H. / Li, Y. / Umezawa, H. / Lin, Y. / Ishimoto, N. / Yun, Y. / Heo, Y. / Park, J.H. / Lee, Y.H. / Park, S.Y.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)13,8991
Polymers13,8991
Non-polymers00
Water00
1
A: Lysozyme C
x 16
A: Lysozyme C

A: Lysozyme C

A: Lysozyme C

A: Lysozyme C

A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)291,87121
Polymers291,87121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation17
identity operation1_555x,y,z4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
50generate(0.999902, -0.014032), (0.014032, 0.999902), (1)1.97431, -1.9468, -9.5334
52generate(0.999975, -0.007016), (0.007016, 0.999975), (1)0.98374, -0.97686, -4.7667
53generate(-0.999994, 0.003508), (-0.003508, -0.999994), (1)278.95003, 279.93033, -2.38335
55generate(-0.999994, -0.003508), (0.003508, -0.999994), (1)279.93033, 278.95003, 2.38335
56generate(0.999975, 0.007016), (-0.007016, 0.999975), (1)-0.97686, 0.98374, 4.7667

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 13898.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Hen egg white lysozyme (HEWL) amyloid / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 2
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.799 ° / Axial rise/subunit: 2.38335 Å / Axial symmetry: C1
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1 / Symmetry type: HELICAL

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