+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12570 | |||||||||
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Title | AL amyloid fibril from a lambda 1 light chain | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Karimi Farsijani S / Radamaker L / Fandrich M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Role of mutations and post-translational modifications in systemic AL amyloidosis studied by cryo-EM. Authors: Lynn Radamaker / Sara Karimi-Farsijani / Giada Andreotti / Julian Baur / Matthias Neumann / Sarah Schreiner / Natalie Berghaus / Raoul Motika / Christian Haupt / Paul Walther / Volker ...Authors: Lynn Radamaker / Sara Karimi-Farsijani / Giada Andreotti / Julian Baur / Matthias Neumann / Sarah Schreiner / Natalie Berghaus / Raoul Motika / Christian Haupt / Paul Walther / Volker Schmidt / Stefanie Huhn / Ute Hegenbart / Stefan O Schönland / Sebastian Wiese / Clarissa Read / Matthias Schmidt / Marcus Fändrich / Abstract: Systemic AL amyloidosis is a rare disease that is caused by the misfolding of immunoglobulin light chains (LCs). Potential drivers of amyloid formation in this disease are post-translational ...Systemic AL amyloidosis is a rare disease that is caused by the misfolding of immunoglobulin light chains (LCs). Potential drivers of amyloid formation in this disease are post-translational modifications (PTMs) and the mutational changes that are inserted into the LCs by somatic hypermutation. Here we present the cryo electron microscopy (cryo-EM) structure of an ex vivo λ1-AL amyloid fibril whose deposits disrupt the ordered cardiomyocyte structure in the heart. The fibril protein contains six mutational changes compared to the germ line and three PTMs (disulfide bond, N-glycosylation and pyroglutamylation). Our data imply that the disulfide bond, glycosylation and mutational changes contribute to determining the fibril protein fold and help to generate a fibril morphology that is able to withstand proteolytic degradation inside the body. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12570.map.gz | 58.5 MB | EMDB map data format | |
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Header (meta data) | emd-12570-v30.xml emd-12570.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12570_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_12570.png | 108.7 KB | ||
Others | emd_12570_half_map_1.map.gz emd_12570_half_map_2.map.gz | 52 MB 51.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12570 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12570 | HTTPS FTP |
-Validation report
Summary document | emd_12570_validation.pdf.gz | 441.1 KB | Display | EMDB validaton report |
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Full document | emd_12570_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | emd_12570_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | emd_12570_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12570 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12570 | HTTPS FTP |
-Related structure data
Related structure data | 7nslMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10730 (Title: AL amyloid fibril from a glycosylated lambda 1 light chain Data size: 495.9 Data #1: Unaligned multi-frame micrographs of AL amyloidosis extracted ex vivo amyloid fibrils patient FOR001 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12570.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: #2
File | emd_12570_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12570_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Amyloid fibril of an antibody lambda 1 immunoglobulin light chain
Entire | Name: Amyloid fibril of an antibody lambda 1 immunoglobulin light chain |
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Components |
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-Supramolecule #1: Amyloid fibril of an antibody lambda 1 immunoglobulin light chain
Supramolecule | Name: Amyloid fibril of an antibody lambda 1 immunoglobulin light chain type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Extracted fibrils from the explanted heart of a patient suffering from systemic AL amyloidosis |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Heart / Tissue: Heart muscle |
-Macromolecule #1: Amyloid lambda1 light chain
Macromolecule | Name: Amyloid lambda1 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Human (human) / Organ: Heart / Tissue: Heart muscle tissue |
Molecular weight | Theoretical: 12.122354 KDa |
Sequence | String: QSVLTQPPSV SAAPGQNVTI SCSGSSSNIG NNYVSWYQQL PGTAPKLLIY ETDKRPSGIP DRFSGSKSGT SATLGITGLQ TADEADYYC GTWESSLLAG VFGGGTKLTV LGQPKAAPS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-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 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
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 |
-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: 3032 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
+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 Target criteria: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) |
Output model | PDB-7nsl: |