[English] 日本語
Yorodumi
- EMDB-66047: ALECT2 type Ib filament from renal biopsy tissue of an individual... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66047
TitleALECT2 type Ib 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: 1.95 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

-
Structure visualization

Supplemental images

emd_66047.png

Downloads & links

-
Map

FileDownload / File: emd_66047.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00905
Minimum - Maximum-0.031348404 - 0.08236334
Average (Standard dev.)0.0002586935 (±0.0043445714)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_66047_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66047_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66047_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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: 3 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.82 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.94 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 67892
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more