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- EMDB-18883: Cryo-EM structure of the D87G lysozyme amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-18883
TitleCryo-EM structure of the D87G lysozyme amyloid fibril
Map data
Sample
  • Complex: LysD87G amyloid fibril
    • Protein or peptide: Lysozyme C
KeywordsLysozyme / amyloid fibril / misfolding disease / cryo-EM / ALys amyloidosis / amyloidogenic variant / PROTEIN FIBRIL
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKarimi-Farsijani S / Sharma K / Schmidt M / Faendrich M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis.
Authors: Sara Karimi-Farsijani / Kartikay Sharma / Marijana Ugrina / Lukas Kuhn / Peter Benedikt Pfeiffer / Christian Haupt / Sebastian Wiese / Ute Hegenbart / Stefan O Schönland / Nadine Schwierz / ...Authors: Sara Karimi-Farsijani / Kartikay Sharma / Marijana Ugrina / Lukas Kuhn / Peter Benedikt Pfeiffer / Christian Haupt / Sebastian Wiese / Ute Hegenbart / Stefan O Schönland / Nadine Schwierz / Matthias Schmidt / Marcus Fändrich /
Abstract: Systemic ALys amyloidosis is a debilitating protein misfolding disease that arises from the formation of amyloid fibrils from C-type lysozyme. We here present a 2.8 Å cryo-electron microscopy ...Systemic ALys amyloidosis is a debilitating protein misfolding disease that arises from the formation of amyloid fibrils from C-type lysozyme. We here present a 2.8 Å cryo-electron microscopy structure of an amyloid fibril, which was isolated from the abdominal fat tissue of a patient who expressed the D87G variant of human lysozyme. We find that the fibril possesses a stable core that is formed by all 130 residues of the fibril precursor protein. There are four disulfide bonds in each fibril protein that connect the same residues as in the globularly folded protein. As the conformation of lysozyme in the fibril is otherwise fundamentally different from native lysozyme, our data provide a structural rationale for the need of protein unfolding in the development of systemic ALys amyloidosis.
History
DepositionNov 13, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18883.png

Downloads & links

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Map

FileDownload / File: emd_18883.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.10786271 - 0.20275515
Average (Standard dev.)0.00008136288 (±0.003099878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18883_additional_1.map
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Half map: #1

Fileemd_18883_half_map_1.map
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Half map: #2

Fileemd_18883_half_map_2.map
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Sample components

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Entire : LysD87G amyloid fibril

EntireName: LysD87G amyloid fibril
Components
  • Complex: LysD87G amyloid fibril
    • Protein or peptide: Lysozyme C

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Supramolecule #1: LysD87G amyloid fibril

SupramoleculeName: LysD87G amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Lysozyme C

MacromoleculeName: Lysozyme C / type: protein_or_peptide / ID: 1 / Details: Variant D87G / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.662658 KDa
SequenceString:
KVFERCELAR TLKRLGMDGY RGISLANWMC LAKWESGYNT RATNYNAGDR STDYGIFQIN SRYWCNDGKT PGAVNACHLS CSALLQGNI ADAVACAKRV VRDPQGIRAW VAWRNRCQNR DVRQYVQGCG V

UniProtKB: Lysozyme C

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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

BufferpH: 7 / Details: pure water
GridModel: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 49.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.78 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 120356
Startup modelType of model: OTHER / Details: cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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