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- EMDB-66048: ALECT2 type IIa filament from renal biopsy tissue of an individua... -

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Basic information

Entry
Database: EMDB / ID: EMD-66048
TitleALECT2 type IIa filament from renal biopsy tissue of an individual with ALECT2 amyloidosis
Map data
Sample
  • Tissue: Leukocyte chemotactic factor 2 amyloid filaments
    • Protein or peptide: Leukocyte cell-derived chemotaxin-2
KeywordsLeukocyte chemotactic factor 2 amyloid filament / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZheng J / Zheng Y / Shi Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82371415 China
National Natural Science Foundation of China (NSFC)82170724 China
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of ALECT2 filaments from human renal biopsies.
Authors: Jian-Lin Zheng / Yu-Xin Zheng / Kai Chen / Shuang Wang / Jia-Wei Liang / Su-Xia Wang / Li Yang / Yang Shi /
Abstract: Leukocyte chemotactic factor 2 is a recently identified amyloidogenic protein, whose abnormal aggregation defines a systemic amyloidosis termed ALECT2 amyloidosis. Due to the lack of reliable ...Leukocyte chemotactic factor 2 is a recently identified amyloidogenic protein, whose abnormal aggregation defines a systemic amyloidosis termed ALECT2 amyloidosis. Due to the lack of reliable biomarkers, diagnosis relies primarily on histological demonstration and typing of amyloid deposits in renal biopsies. However, immunohistochemical detection of ALECT2 is often inconsistent, leading to diagnostic uncertainty. The underlying basis remains poorly understood, reflecting our limited knowledge of ALECT2 deposits. Here, using cryo-electron microscopy (cryo-EM), we determined the structures of ALECT2 filaments from renal biopsies of five living patients. Unlike filaments assembled from recombinant proteins in vitro, all 133 residues of mature LECT2 are incorporated into the filament cores, with native disulfide linkages preserved. The filaments consistently adopt the shared six-layered folds in all five patients, indicating a common mechanism of amyloidogenesis. Because all residues are incorporated into the fibril core, epitope accessibility is limited. This can explain variability in immunohistochemical detection and thus highlights the need for conformation-specific antibodies and antibody-independent detection strategies for improving diagnostic accuracy. This biopsy-based workflow not only expands the availability of patient-derived tissue for cryo-EM studies but also demonstrates the potential of cryo-EM as a tool for precise diagnosis of systemic amyloidosis.
History
DepositionSep 2, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66048.png

Downloads & links

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Map

FileDownload / File: emd_66048.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00792
Minimum - Maximum-0.021456208 - 0.041759394
Average (Standard dev.)0.00038239188 (±0.0029912589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66048_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_66048_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66048_half_map_2.map
Projections & Slices
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Sample components

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Entire : Leukocyte chemotactic factor 2 amyloid filaments

EntireName: Leukocyte chemotactic factor 2 amyloid filaments
Components
  • Tissue: Leukocyte chemotactic factor 2 amyloid filaments
    • Protein or peptide: Leukocyte cell-derived chemotaxin-2

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Supramolecule #1: Leukocyte chemotactic factor 2 amyloid filaments

SupramoleculeName: Leukocyte chemotactic factor 2 amyloid filaments / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Leukocyte cell-derived chemotaxin-2

MacromoleculeName: Leukocyte cell-derived chemotaxin-2 / type: protein_or_peptide / ID: 1
Details: Leukocyte chemotactic factor 2 with a I40V mutation
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.593726 KDa
SequenceString:
GPWANICAGK SSNEIRTCDR HGCGQYSAQR SQRPHQGVDV LCSAGSTVYA PFTGMIVGQE KPYQNKNAIN NGVRISGRGF CVKMFYIKP IKYKGPIKKG EKLGTLLPLQ KVYPGIQSHV HIENCDSSDP TAYL

UniProtKB: Leukocyte cell-derived chemotaxin-2

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.77 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.91 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 59401
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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