[English] 日本語
Yorodumi- EMDB-3128: Structure of a cross-beta amyloid fibril from IGSNVVTWYQQL peptid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3128 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a cross-beta amyloid fibril from IGSNVVTWYQQL peptide of AL-DIA immunoglobulin light chain by cryo-EM and fiber diffraction | |||||||||
Map data | Reconstruction morphology 1 of a left-handed amyloid-like fibril of the IGSNVVTWYQQL fragment of an immunoglobulin light chain | |||||||||
Sample |
| |||||||||
Keywords | AL amyloidosis / cryo electron microscopy / steric zipper / three dimensional reconstruction | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | Schmidt A / Annamalai K / Schmidt M / Grigorieff N / Fandrich M | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril. Authors: Andreas Schmidt / Karthikeyan Annamalai / Matthias Schmidt / Nikolaus Grigorieff / Marcus Fändrich / Abstract: Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but ...Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3128.map.gz | 2.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3128-v30.xml emd-3128.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3128_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_3128.png | 16.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3128 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3128 | HTTPS FTP |
-Validation report
Summary document | emd_3128_validation.pdf.gz | 219.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3128_full_validation.pdf.gz | 218.4 KB | Display | |
Data in XML | emd_3128_validation.xml.gz | 10.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3128 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3128 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_3128.map.gz / Format: CCP4 / Size: 2.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction morphology 1 of a left-handed amyloid-like fibril of the IGSNVVTWYQQL fragment of an immunoglobulin light chain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...
Entire | Name: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of Human AL Patient |
---|---|
Components |
|
-Supramolecule #1000: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...
Supramolecule | Name: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of Human AL Patient type: sample / ID: 1000 / Details: The sample forms long amyloid-like fibrils. / Number unique components: 1 |
---|
-Macromolecule #1: Immunoglobulin Light Chain
Macromolecule | Name: Immunoglobulin Light Chain / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Plasma Cell / Location in cell: extracellular |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 5.0 mg/mL |
---|---|
Buffer | pH: 8 / Details: 50mM Tris-HCL |
Grid | Details: C-flat 1.2/1.3-2C 400 mesh grids, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 50 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 Method: Incubation of 0.014 mg/ml fibril solution on glow discharged holey carbon grid for 30 seconds and backside blotting for 4 seconds before plunging. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Temperature | Average: 100 K |
Date | Nov 12, 2012 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Number real images: 10 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 66350.7 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |