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- PDB-9lix: The cryo-EM structure of amyloid fibrils from abdominal fat of an... -

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Basic information

Entry
Database: PDB / ID: 9lix
TitleThe cryo-EM structure of amyloid fibrils from abdominal fat of an AL amyloidosis patient (case 2) - polymorph 1.
ComponentsMonoclonal immunoglobulin light chains (LC)
KeywordsPROTEIN FIBRIL / amyloid
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsYao, Y.X. / Zhao, Q.Y. / Liu, C. / Li, D.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Monoclonal immunoglobulin light chains (LC)
C: Monoclonal immunoglobulin light chains (LC)
E: Monoclonal immunoglobulin light chains (LC)
A: Monoclonal immunoglobulin light chains (LC)
F: Monoclonal immunoglobulin light chains (LC)
B: Monoclonal immunoglobulin light chains (LC)


Theoretical massNumber of molelcules
Total (without water)95,7936
Polymers95,7936
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody
Monoclonal immunoglobulin light chains (LC)


Mass: 15965.562 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: amyloid light chain / Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding 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: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.4 ° / Axial rise/subunit: 2.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15087 / Symmetry type: HELICAL

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