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- PDB-9non: Cryo-EM structure of amyloid fibril isolated from the kidney of a... -

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Basic information

Entry
Database: PDB / ID: 9non
TitleCryo-EM structure of amyloid fibril isolated from the kidney of a variant Alect2-I40V amyloidosis patient
ComponentsLeukocyte cell-derived chemotaxin-2
KeywordsPROTEIN FIBRIL / Leukocyte cell-derived chemotaxin-2 / LECT2 / systemic amyloidosis / ALECT2 / systemic / amyloid / kidney.
Function / homology
Function and homology information


skeletal system development / chemotaxis / : / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Leukocyte cell-derived chemotaxin 2 / Leukocyte cell-derived chemotaxin 2, chordata / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
Leukocyte cell-derived chemotaxin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNguyen, B. / Saelices, L.
Funding support United States, 3items
OrganizationGrant numberCountry
American Heart Association847236 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DP2-HL163810 United States
Welch FoundationI-2121-20220331 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural polymorphism of ex-vivo ALECT2 amyloid fibrils revealed by cryo-EM.
Authors: Shumaila Afrin / Binh An Nguyen / Virender Singh / Preeti Singh / Parker Bassett / Maja Pekala / Bret Evers / Christian Lopez / Yasmin Ahmed / Li Li / Raja Reddy Kallem / Andrew Lemoff / ...Authors: Shumaila Afrin / Binh An Nguyen / Virender Singh / Preeti Singh / Parker Bassett / Maja Pekala / Bret Evers / Christian Lopez / Yasmin Ahmed / Li Li / Raja Reddy Kallem / Andrew Lemoff / Christos Argyropoulos / Barbara Kluve-Beckerman / Lorena Saelices /
Abstract: ALECT2 amyloidosis is a rare systemic disease characterized by the pathological deposition of leukocyte cell-derived chemotaxin-2 (LECT2) as amyloid fibrils, primarily affecting the kidneys and liver. ...ALECT2 amyloidosis is a rare systemic disease characterized by the pathological deposition of leukocyte cell-derived chemotaxin-2 (LECT2) as amyloid fibrils, primarily affecting the kidneys and liver. The molecular mechanisms underlying LECT2 aggregation remain poorly defined, hindering diagnostic and therapeutic development. Here, we present cryo-electron microscopy structures of ex-vivo ALECT2 fibrils extracted from a patient's kidney. We identified three fibril polymorphs: a predominant single-protofilament morphology and two minor double-protofilament morphologies. The dominant single-protofilament morphology comprises the full-length 133-residue LECT2 protein and retains all three native disulfide bonds. Low-resolution reconstructions of double-protofilament morphologies suggest they adopt a similar fold to the single protofilament morphology, but form paired assemblies with different inter-filament interfaces. Mass spectrometry also reveals acetylation within the fibrils. These findings offer critical insights into the structural basis of ALECT2 amyloid formation and identify molecular features that could inform future diagnostic and therapeutic approaches.
History
DepositionMar 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Leukocyte cell-derived chemotaxin-2
C: Leukocyte cell-derived chemotaxin-2
A: Leukocyte cell-derived chemotaxin-2
D: Leukocyte cell-derived chemotaxin-2
E: Leukocyte cell-derived chemotaxin-2


Theoretical massNumber of molelcules
Total (without water)72,9695
Polymers72,9695
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: Protein
Leukocyte cell-derived chemotaxin-2 / LECT-2 / hLECT2


Mass: 14593.726 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Kidney / Tissue: Kidney / References: UniProt: O14960
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: Leukocyte cell-derived chemotaxin-2 protein / Type: COMPLEX
Details: fibrillation of Leukocyte cell-derived chemotaxin-2 protein
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
Buffer solutionpH: 7 / Details: extracted in water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: 2600 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 3.69 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 22899

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPU3.5image acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.1model fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -0.91 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 179392
Details: We used Relion built-in Topaz to autopick this dataset.
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36221 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 45 / Protocol: OTHER / Space: REAL
Details: We used ModelAngelo to obtain the initial fibril model of a single chain.
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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