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- EMDB-11030: AL amyloid fibril from a lambda 3 light chain in conformation B -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11030 | |||||||||
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Title | AL amyloid fibril from a lambda 3 light chain in conformation B | |||||||||
![]() | EM map of amyloid fibril from a patient-derived lambda 3 immunoglobulin light chain conformation B | |||||||||
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Function / homology | ![]() CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Radamaker L / Fandrich M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM reveals structural breaks in a patient-derived amyloid fibril from systemic AL amyloidosis. Authors: Lynn Radamaker / Julian Baur / Stefanie Huhn / Christian Haupt / Ute Hegenbart / Stefan Schönland / Akanksha Bansal / Matthias Schmidt / Marcus Fändrich / ![]() Abstract: Systemic AL amyloidosis is a debilitating and potentially fatal disease that arises from the misfolding and fibrillation of immunoglobulin light chains (LCs). The disease is patient-specific with ...Systemic AL amyloidosis is a debilitating and potentially fatal disease that arises from the misfolding and fibrillation of immunoglobulin light chains (LCs). The disease is patient-specific with essentially each patient possessing a unique LC sequence. In this study, we present two ex vivo fibril structures of a λ3 LC. The fibrils were extracted from the explanted heart of a patient (FOR005) and consist of 115-residue fibril proteins, mainly from the LC variable domain. The fibril structures imply that a 180° rotation around the disulfide bond and a major unfolding step are necessary for fibrils to form. The two fibril structures show highly similar fibril protein folds, differing in only a 12-residue segment. Remarkably, the two structures do not represent separate fibril morphologies, as they can co-exist at different z-axial positions within the same fibril. Our data imply the presence of structural breaks at the interface of the two structural forms. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 91.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 50.4 KB | ||
Others | ![]() ![]() | 10.3 MB 10.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z1iMC ![]() 6z1oC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Raw cryo-EM movies of AL fibrils extracted from human heart tissue [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM map of amyloid fibril from a patient-derived lambda 3 immunoglobulin light chain conformation B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_11030_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11030_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Amyloid fibril of an antibody lambda 3 immunoglobulin light chain
Entire | Name: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain |
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Components |
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-Supramolecule #1: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain
Supramolecule | Name: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Extracted fibrils from the explanted heart of a systemic AL amyloidosis patient |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: lambda 3 light chain fragment, residues 2-116
Macromolecule | Name: lambda 3 light chain fragment, residues 2-116 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.664521 KDa |
Sequence | String: AVSVALGQTV RITCQGDSLR SYSASWYQQK PGQAPVLVIF RNTASLTITG AQAEDEADYY CNSRDSSANH QVFGGGTKLT V |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7 / Component - Formula: H2O / Component - Name: Distilled water |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Details: 40 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III / Details: blot for 9s before plunging. |
Details | Sample in pure water, pH not determined |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 1964 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Secondary structure restraints and NCS were applied during refinement |
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Refinement | Space: REAL / Protocol: OTHER / Overall B value: 73.24 Target criteria: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) |
Output model | ![]() PDB-6z1i: |