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- EMDB-48160: Light chain amyloidosis amyloid fibril - IGLV6-57 -

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Basic information

Entry
Database: EMDB / ID: EMD-48160
TitleLight chain amyloidosis amyloid fibril - IGLV6-57
Map dataThe masked, post-processed single protofilament structure map cut to five layers of the amyloid fibril.
Sample
  • Tissue: Ex vivo amyloid fibrils from cardiac tissue
    • Protein or peptide: Antibody light chain
KeywordsLight chain / amyloid / IGLV6 / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsBassett PT / Saelices L
Funding support United States, 5 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
Other privateUTSW Endowment United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: To Be Published
Title: Structure of ex vivo cardiac AL amyloidosis fibrils derived from IGLV6-57 germline.
Authors: Bassett PT / Saelices L
History
DepositionDec 4, 2024-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48160.png

Downloads & links

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Map

FileDownload / File: emd_48160.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe masked, post-processed single protofilament structure map cut to five layers of the amyloid fibril.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 256 pix.
= 250.88 Å		0.98 Å/pix.
x 256 pix.
= 250.88 Å		0.98 Å/pix.
x 256 pix.
= 250.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.13698223 - 0.22971484
Average (Standard dev.)0.00037330427 (±0.005688155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 250.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48160_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The masked, post-processed single protofilament structure map cut...

Fileemd_48160_additional_1.map
AnnotationThe masked, post-processed single protofilament structure map cut to five layers of the amyloid fibril.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The masked, post-processed single protofilament structure map cut...

Fileemd_48160_additional_2.map
AnnotationThe masked, post-processed single protofilament structure map cut to five layers of the amyloid fibril.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The masked, post-processed single protofilament structure map cut...

Fileemd_48160_half_map_1.map
AnnotationThe masked, post-processed single protofilament structure map cut to five layers of the amyloid fibril.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The masked, post-processed single protofilament structure map cut...

Fileemd_48160_half_map_2.map
AnnotationThe masked, post-processed single protofilament structure map cut to five layers of the amyloid fibril.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ex vivo amyloid fibrils from cardiac tissue

EntireName: Ex vivo amyloid fibrils from cardiac tissue
Components
  • Tissue: Ex vivo amyloid fibrils from cardiac tissue
    • Protein or peptide: Antibody light chain

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Supramolecule #1: Ex vivo amyloid fibrils from cardiac tissue

SupramoleculeName: Ex vivo amyloid fibrils from cardiac tissue / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: Heart / Tissue: Cardiac

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Macromolecule #1: Antibody light chain

MacromoleculeName: Antibody light chain / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 12.142193 KDa
SequenceString:
NFMLTQPHSV SESPGKTVTI SCTRSSGSIA SSYVQWYQQR PGSAPTTVIY EDDERPSGVP DRFSGSIDSS SNSASLTISG LKKEDEAEY YCQSYENSNL YVVFGGGTKL TVL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / 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 reconstructionApplied symmetry - Helical parameters - Δz: 5.03 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.03 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 56955
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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