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- EMDB-11031: AL amyloid fibril from a lambda 3 light chain in conformation A -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11031 | |||||||||
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Title | AL amyloid fibril from a lambda 3 light chain in conformation A | |||||||||
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![]() | Amyloid fibril of an antibody lambda 3 immunoglobulin light chain
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Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / ![]() | |||||||||
![]() | 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. | |||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Others |
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Archive directory |
-Related structure data
Related structure data | ![]() 6z1oCM ![]() 6z1iC C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: #1
File | emd_11031_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11031_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 Details: Extracted fibrils from the explanted heart of a systemic AL amyloidosis patient Number of components: 2 |
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-Component #1: protein, Amyloid fibril of an antibody lambda 3 immunoglobulin li...
Protein | Name: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain Details: Extracted fibrils from the explanted heart of a systemic AL amyloidosis patient Recombinant expression: No |
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Source | Species: ![]() ![]() |
Source (natural) | Organ or tissue: Heart |
-Component #2: protein, lambda 3 immunoglobulin light chain fragment, residues 2-116
Protein | Name: lambda 3 immunoglobulin light chain fragment, residues 2-116 Number of Copies: 6 / Recombinant expression: No |
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Mass | Theoretical: 9.431303 kDa |
Source | Species: ![]() ![]() |
Source (natural) | Organ or tissue: Heart |
-Experimental details
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Sample preparation
Specimen | Specimen state: Filament / Method: ![]() |
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Helical parameters | Axial symmetry: C1 (asymmetric) / Delta z: 4.8 Å / Delta phi: -1.1 %deg; |
Sample solution | pH: 7 |
Support film | 40 mA |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 95 % / Details: blot for 9s before plunging. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Cs: 2.7 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
-Image acquisition
Image acquisition | Number of digital images: 1964 |
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Image processing
-Atomic model buiding
Modeling #1 | Target criteria: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) Refinement space: REAL Details: Secondary structure restraints and NCS were applied during refinement Overall bvalue: 73.24 |
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Output model |