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- EMDB-63127: The cryo-EM structure of amyloid fibrils from abdominal fat of an... -

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Basic information

Entry
Database: EMDB / ID: EMD-63127
TitleThe cryo-EM structure of amyloid fibrils from abdominal fat of an AL amyloidosis patient (case 2) - polymorph 2.
Map data
Sample
  • Tissue: amyloid light chain
    • Protein or peptide: Monoclonal immunoglobulin light chains (LC)
Keywordsamyloid / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYao YX / Zhao QY / Liu C / Li D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Biopsy-resolved cryo-EM structures of amyloid fibrils provide molecular insights into AL amyloidosis.
Authors: Yuxuan Yao / Qinyue Zhao / Shun Yao / Yamei Xu / Kaien Liu / Tianyi Cao / Bo Sun / Jingmin Zhou / Cong Liu / Dan Li /
Abstract: Systemic light chain amyloidosis (AL) is characterized by amyloid fibril deposition in multiple organs, often severely affecting cardiac function. In this study, we extracted amyloid fibrils directly ...Systemic light chain amyloidosis (AL) is characterized by amyloid fibril deposition in multiple organs, often severely affecting cardiac function. In this study, we extracted amyloid fibrils directly from abdominal fat and cardiac tissue biopsies obtained from three AL patients. Using cryo-electron microscopy, we determined five distinct structures of light chain (LC) amyloid fibrils. Our results demonstrate that LC fibrils from different patients adopt unique structural conformations, highlighting patient-specific fibril variations. Conversely, LC fibrils extracted from different tissues within the same patient share highly similar overall fibril structures, yet exhibit localized conformational variations, potentially shaped by distinct environmental cofactors. This study emphasizes the combined roles of patient-specific protein sequences and tissue-specific microenvironments in defining LC fibril conformation. The determination of LC fibril structures directly from easily accessible abdominal fat biopsy provides critical molecular insights into AL amyloidosis pathology, facilitating the development of therapeutic strategies.
History
DepositionJan 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63127.png

Downloads & links

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Map

FileDownload / File: emd_63127.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.028027048 - 0.05968497
Average (Standard dev.)0.000085710664 (±0.002275836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63127_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_63127_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : amyloid light chain

EntireName: amyloid light chain
Components
  • Tissue: amyloid light chain
    • Protein or peptide: Monoclonal immunoglobulin light chains (LC)

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Supramolecule #1: amyloid light chain

SupramoleculeName: amyloid light chain / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Monoclonal immunoglobulin light chains (LC)

MacromoleculeName: Monoclonal immunoglobulin light chains (LC) / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.965562 KDa
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGSNSNIG GNTVTWYQHL PGTAPKLLIY SNNQWPSGVP DRFSGSKSGT SASLAISGLQ SDDEGDYYC ATWDDSLSGP VFGGGTKLTV LGQPKNAPSV TLFPPSSQRS SLFERLQPLI SDFYPGAVTV AWK

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 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: 2.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12758
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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