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- EMDB-70557: Cardiac lambda-6 light chain amyloid AL-224L single protofilament -

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Basic information

Entry
Database: EMDB / ID: EMD-70557
TitleCardiac lambda-6 light chain amyloid AL-224L single protofilament
Map dataunsharpened map
Sample
  • Complex: Cardiac tissue-derived immunoglobulin l6 light chain AL-224L
    • Protein or peptide: Immunoglobulin l6 light-chain AL-224L
Keywordsamyloid / heart / immunoglobulin / light-chain / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsHicks CW / Gursky O / Huda N
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD032253 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135158 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM067260 United States
CitationJournal: J Mol Biol / Year: 2025
Title: Cryo-EM of Cardiac AL-224L Amyloid Reveals Shared Structural Motifs and Mutation-induced Differences in λ6 Light Chain Fibrils.
Authors: Chad W Hicks / Tatiana Prokaeva / Brian Spencer / Shobini Jayaraman / Noorul Huda / Sherry Wong / Hui Chen / Vaishali Sanchorawala / Francesca Lavatelli / Olga Gursky /
Abstract: In light chain amyloidosis (AL), aberrant monoclonal antibody light chains (LCs) deposit in vital organs causing organ damage. Each AL patient features a unique LC; previous cryogenic electron ...In light chain amyloidosis (AL), aberrant monoclonal antibody light chains (LCs) deposit in vital organs causing organ damage. Each AL patient features a unique LC; previous cryogenic electron microscopy (cryo-EM) studies revealed different amyloid structures in different AL patients. How LC mutations influence amyloid structures remains unclear. We report a cryo-EM structure of cardiac AL-224L amyloid (2.92 Å resolution) from λ6-LC family, which is overrepresented in AL amyloidosis. Comparison with λ6-LC structures from two other patients reveals similarities in amyloid folds, along with major differences caused by specific mutations. Differences in AL-224L include altered C-terminal conformation with an exposed surface forming an apparent ligand-binding site; an enlarged hydrophilic pore with orphan density; and altered steric zipper registry with backbone flipping, which likely represent general adaptive mechanisms in amyloids. The results reveal shared features in λ6-LC amyloid folds and suggest how mutation-induced structural changes influence amyloid-ligand interactions in a patient-specific manner.
History
DepositionMay 9, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70557.png

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Map

FileDownload / File: emd_70557.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.12563717 - 0.26864263
Average (Standard dev.)0.00214504 (±0.012556882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70557_msk_1.map
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Additional map: sharpened map B-factor -200

Fileemd_70557_additional_1.map
Annotationsharpened map B-factor -200
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Additional map: sharpened map B-factor -25.8

Fileemd_70557_additional_2.map
Annotationsharpened map B-factor -25.8
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Half map: EM half-map A

Fileemd_70557_half_map_1.map
AnnotationEM half-map A
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Half map: EM half-map B

Fileemd_70557_half_map_2.map
AnnotationEM half-map B
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Sample components

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Entire : Cardiac tissue-derived immunoglobulin l6 light chain AL-224L

EntireName: Cardiac tissue-derived immunoglobulin l6 light chain AL-224L
Components
  • Complex: Cardiac tissue-derived immunoglobulin l6 light chain AL-224L
    • Protein or peptide: Immunoglobulin l6 light-chain AL-224L

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Supramolecule #1: Cardiac tissue-derived immunoglobulin l6 light chain AL-224L

SupramoleculeName: Cardiac tissue-derived immunoglobulin l6 light chain AL-224L
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: heart

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Macromolecule #1: Immunoglobulin l6 light-chain AL-224L

MacromoleculeName: Immunoglobulin l6 light-chain AL-224L / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.467476 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NFMLTQPHSV SESPGKTITI SCTRSSGSIA SNYVQWYQQR PGSAPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLTISG LQTEDEADY YCQSYDSSNP HVVFGGGTKL TVLGQPK

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.86 Å
Applied symmetry - Helical parameters - Δ&Phi: 1.20 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214100
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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