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- EMDB-19818: AL amyloid fibril from the FOR103 light chain -

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Basic information

Entry
Database: EMDB / ID: EMD-19818
TitleAL amyloid fibril from the FOR103 light chain
Map data
Sample
  • Complex: lambda 3 immunoglobulin light chain fragment
    • Protein or peptide: lambda 3 immunoglobulin light chain fragment, residues 2-116
KeywordsAmyloid fibril / AL amyloid / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsPfeiffer PB / Karimi-Farsijani S / Kupfer N / Schmidt M / Faendrich M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Light chain mutations contribute to defining the fibril morphology in systemic AL amyloidosis.
Authors: Sara Karimi-Farsijani / Peter Benedikt Pfeiffer / Sambhasan Banerjee / Julian Baur / Lukas Kuhn / Niklas Kupfer / Ute Hegenbart / Stefan O Schönland / Sebastian Wiese / Christian Haupt / ...Authors: Sara Karimi-Farsijani / Peter Benedikt Pfeiffer / Sambhasan Banerjee / Julian Baur / Lukas Kuhn / Niklas Kupfer / Ute Hegenbart / Stefan O Schönland / Sebastian Wiese / Christian Haupt / Matthias Schmidt / Marcus Fändrich /
Abstract: Systemic AL amyloidosis is one of the most frequently diagnosed forms of systemic amyloidosis. It arises from mutational changes in immunoglobulin light chains. To explore whether these mutations may ...Systemic AL amyloidosis is one of the most frequently diagnosed forms of systemic amyloidosis. It arises from mutational changes in immunoglobulin light chains. To explore whether these mutations may affect the structure of the formed fibrils, we determine and compare the fibril structures from several patients with cardiac AL amyloidosis. All patients are affected by light chains that contain an IGLV3-19 gene segment, and the deposited fibrils differ by the mutations within this common germ line background. Using cryo-electron microscopy, we here find different fibril structures in each patient. These data establish that the mutations of amyloidogenic light chains contribute to defining the fibril architecture and hence the structure of the pathogenic agent.
History
DepositionMar 8, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19818.png

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Map

FileDownload / File: emd_19818.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0244
Minimum - Maximum-0.041957997 - 0.08603669
Average (Standard dev.)0.0001550887 (±0.00216252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19818_msk_1.map
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Half map: #1

Fileemd_19818_half_map_1.map
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Half map: #2

Fileemd_19818_half_map_2.map
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Sample components

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Entire : lambda 3 immunoglobulin light chain fragment

EntireName: lambda 3 immunoglobulin light chain fragment
Components
  • Complex: lambda 3 immunoglobulin light chain fragment
    • Protein or peptide: lambda 3 immunoglobulin light chain fragment, residues 2-116

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Supramolecule #1: lambda 3 immunoglobulin light chain fragment

SupramoleculeName: lambda 3 immunoglobulin light chain fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: residues 2-116
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: lambda 3 immunoglobulin light chain fragment, residues 2-116

MacromoleculeName: lambda 3 immunoglobulin light chain fragment, residues 2-116
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.202262 KDa
SequenceString:
SELTQDPAVS VALGQTVRIT CQGDSLRSYY ASWYQQKSGQ APVLVIYSYN NRPSGIPDRF SGSNSGNTAS LTITGAQAED EADYYCNSR DSSGHHLVFG GGTKLTVLGQ PKAAPS

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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 / Details: water
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2788 / Average exposure time: 10.0 sec. / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.752 Å
Applied symmetry - Helical parameters - Δ&Phi: 1.309 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 120039
Segment selectionNumber selected: 157862 / Software - Name: RELION (ver. 3.1.3)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: correlation coefficient
Output model

PDB-9eme:
AL amyloid fibril from the FOR103 light chain

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