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- EMDB-49601: Cryo-EM structure of amyloid fibril isolated from the kidney of a... -

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Basic information

Entry
Database: EMDB / ID: EMD-49601
TitleCryo-EM structure of amyloid fibril isolated from the kidney of a variant Alect2-I40V amyloidosis patient
Map dataThis map was used for building model.
Sample
  • Complex: Leukocyte cell-derived chemotaxin-2 protein
    • Protein or peptide: Leukocyte cell-derived chemotaxin-2
KeywordsLeukocyte cell-derived chemotaxin-2 / LECT2 / systemic amyloidosis / ALECT2 / systemic / amyloid / kidney. / PROTEIN FIBRIL
Function / homology
Function and homology information


skeletal system development / chemotaxis / extracellular space / 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: 2.4 Å
AuthorsNguyen B / Saelices L
Funding support United States, 3 items
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: To Be Published
Title: Cryo-EM structure of amyloid fibril isolated from the kidney of a variant Alect2-I40V amyloidosis patient
Authors: Nguyen B / Saelices L
History
DepositionMar 10, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49601.png

Downloads & links

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Map

FileDownload / File: emd_49601.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map was used for building model.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 286.2 Å		0.95 Å/pix.
x 300 pix.
= 286.2 Å		0.95 Å/pix.
x 300 pix.
= 286.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.954 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0364
Minimum - Maximum-0.111045435 - 0.21652387
Average (Standard dev.)0.00017162474 (±0.0053487103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 286.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: combined map from two half-maps

Fileemd_49601_additional_1.map
Annotationcombined map from two half-maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map2

Fileemd_49601_half_map_1.map
Annotationhalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map1

Fileemd_49601_half_map_2.map
Annotationhalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Leukocyte cell-derived chemotaxin-2 protein

EntireName: Leukocyte cell-derived chemotaxin-2 protein
Components
  • Complex: Leukocyte cell-derived chemotaxin-2 protein
    • Protein or peptide: Leukocyte cell-derived chemotaxin-2

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Supramolecule #1: Leukocyte cell-derived chemotaxin-2 protein

SupramoleculeName: Leukocyte cell-derived chemotaxin-2 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: fibrillation of Leukocyte cell-derived chemotaxin-2 protein
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney

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Macromolecule #1: Leukocyte cell-derived chemotaxin-2

MacromoleculeName: Leukocyte cell-derived chemotaxin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
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 / Details: extracted in water
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 22899 / Average exposure time: 3.69 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.91 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 36221
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Segment selectionNumber selected: 179392 / Software - Name: RELION (ver. 4.0)
Details: We used Relion built-in Topaz to autopick this dataset.
Startup modelType of model: INSILICO MODEL / In silico model: generated using relion_helix_inimodel2d
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsWe used ModelAngelo to obtain the initial fibril model of a single chain.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 45
Output model

PDB-9non:
Cryo-EM structure of amyloid fibril isolated from the kidney of a variant Alect2-I40V amyloidosis patient

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