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- EMDB-29682: Cryo-EM structure of recombinant human LECT2 amyloid fibril core -

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Basic information

Entry
Database: EMDB / ID: EMD-29682
TitleCryo-EM structure of recombinant human LECT2 amyloid fibril core
Map dataCryo-EM map of human LECT2 amyloid fibrils.
Sample
  • Complex: Recombinant human LECT2 amyloid fibril core.
    • Protein or peptide: Leukocyte cell-derived chemotaxin-2
Keywordsamyloid / LECT2 / human / recombinant / fibril / protein / ALECT2 / cryo-EM / PROTEIN FIBRIL
Function / homology
Function and homology information


skeletal system development / chemotaxis / extracellular space / identical protein binding / metal ion 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: 2.715 Å
AuthorsRichards LS / Flores MD / Zink S / Schibrowsky NA / Sawaya MR / Rodriguez JA
Funding support United States, 5 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Grant R35 GM128867 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5T32GM008496 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U24 GM129541 United States
CitationJournal: Structure / Year: 2023
Title: Cryo-EM structure of a human LECT2 amyloid fibril reveals a network of polar ladders at its core.
Authors: Logan S Richards / Maria D Flores / Samantha Zink / Natalie A Schibrowsky / Michael R Sawaya / Jose A Rodriguez /
Abstract: ALECT2 systemic amyloidosis is associated with deposition of the leukocyte cell-derived chemotaxin-2 (LECT2) protein in the form of fibrils. In ALECT2 amyloidosis, ALECT2 fibrils deposit in the ...ALECT2 systemic amyloidosis is associated with deposition of the leukocyte cell-derived chemotaxin-2 (LECT2) protein in the form of fibrils. In ALECT2 amyloidosis, ALECT2 fibrils deposit in the glomerulus, resulting in renal failure. Patients lack effective treatment options outside of renal transplant or dialysis. The structure of globular LECT2 has been determined but structures of ALECT2 amyloid fibrils remain unknown. Using single-particle cryo-EM, we find that recombinant human LECT2 forms robust twisting fibrils with canonical amyloid features. ALECT2 fibrils contain two mating protofilaments spanning residues 55-75 of the LECT2 sequence. The geometry of the ALECT2 fibril displays features in line with other pathogenic amyloids. Its core is tightly packed and stabilized by both hydrophobic contacts and hydrogen-bonded uncharged polar residues. The robustness of ALECT2 fibril cores is illustrated by their resistance to denaturants and proteases. This ALECT2 fibril structure presents a potential new target for treatments against ALECT2 systemic amyloidosis.
History
DepositionFeb 6, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29682.png

Downloads & links

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Map

FileDownload / File: emd_29682.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of human LECT2 amyloid fibrils.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 384 pix.
= 306.816 Å		0.8 Å/pix.
x 384 pix.
= 306.816 Å		0.8 Å/pix.
x 384 pix.
= 306.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.799 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0315
Minimum - Maximum-0.058871806 - 0.117378704
Average (Standard dev.)0.0000033512963 (±0.0033824318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 306.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_29682_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_29682_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Recombinant human LECT2 amyloid fibril core.

EntireName: Recombinant human LECT2 amyloid fibril core.
Components
  • Complex: Recombinant human LECT2 amyloid fibril core.
    • Protein or peptide: Leukocyte cell-derived chemotaxin-2

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Supramolecule #1: Recombinant human LECT2 amyloid fibril core.

SupramoleculeName: Recombinant human LECT2 amyloid fibril core. / type: complex / 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 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.389752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIVGQEKPYQ NKNAINNGVR I

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: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.345 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.49 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.715 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 24770
Segment selectionNumber selected: 1622942 / Software - Name: crYOLO
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8g2v:
Cryo-EM structure of recombinant human LECT2 amyloid fibril core

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