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- PDB-9oka: Cardiac lambda-6 light chain amyloid AL-224L single protofilament -

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Basic information

Entry
Database: PDB / ID: 9oka
TitleCardiac lambda-6 light chain amyloid AL-224L single protofilament
ComponentsImmunoglobulin l6 light-chain AL-224L
KeywordsPROTEIN FIBRIL / amyloid / heart / immunoglobulin / light-chain
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsHicks, C.W. / Gursky, O. / Huda, N.
Funding support United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Immunoglobulin l6 light-chain AL-224L
C: Immunoglobulin l6 light-chain AL-224L
D: Immunoglobulin l6 light-chain AL-224L
B: Immunoglobulin l6 light-chain AL-224L
A: Immunoglobulin l6 light-chain AL-224L


Theoretical massNumber of molelcules
Total (without water)62,3375
Polymers62,3375
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 12467.476 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: 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: Cardiac tissue-derived immunoglobulin l6 light chain AL-224L
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Organ: heart
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: dev_4788 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 1.2 ° / Axial rise/subunit: 4.86 Å / Axial symmetry: C1
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214100 / Symmetry type: HELICAL
RefinementHighest resolution: 2.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023410
ELECTRON MICROSCOPYf_angle_d0.5334635
ELECTRON MICROSCOPYf_dihedral_angle_d4.543465
ELECTRON MICROSCOPYf_chiral_restr0.044505
ELECTRON MICROSCOPYf_plane_restr0.003610

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