+Open data
-Basic information
Entry | Database: PDB / ID: 8r47 | ||||||
---|---|---|---|---|---|---|---|
Title | AL amyloid fibril from the FOR010 light chain | ||||||
Components | lambda 3 immunoglobulin light chain fragment, residues 4-116 | ||||||
Keywords | PROTEIN FIBRIL / Amyloid fibril / AL amyloid | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.25 Å | ||||||
Authors | Pfeiffer, P.B. / Banerjee, S. / Schmidt, M. / Faendrich, M. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8r47.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8r47.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 8r47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r47_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8r47_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8r47_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 8r47_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/8r47 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/8r47 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Antibody | Mass: 12063.337 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: lambda 3 immunoglobulin light chain fragment / Type: COMPLEX / Details: residues 4-116 / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Buffer component | Name: Water / Formula: H2O |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4008 |
-Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -1.4634 ° / Axial rise/subunit: 4.76311 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 414351 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51394 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient |