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Yorodumi- EMDB-3990: Morphology VI - cross-beta amyloid fibril structure from the IGSN... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3990 | |||||||||
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Title | Morphology VI - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 13.4 Å | |||||||||
Authors | Close W / Faendrich M | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Physical basis of amyloid fibril polymorphism. Authors: William Close / Matthias Neumann / Andreas Schmidt / Manuel Hora / Karthikeyan Annamalai / Matthias Schmidt / Bernd Reif / Volker Schmidt / Nikolaus Grigorieff / Marcus Fändrich / Abstract: Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based ...Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures. | |||||||||
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_3990.map.gz | 46.3 MB | EMDB map data format | |
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Header (meta data) | emd-3990-v30.xml emd-3990.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3990_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_3990.png | 51.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3990 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3990 | HTTPS FTP |
-Validation report
Summary document | emd_3990_validation.pdf.gz | 206.4 KB | Display | EMDB validaton report |
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Full document | emd_3990_full_validation.pdf.gz | 205.5 KB | Display | |
Data in XML | emd_3990_validation.xml.gz | 10.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3990 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3990 | HTTPS FTP |
-Related structure data
Related structure data | 3986C 3987C 3988C 3989C 3991C 3992C 3993C 3994C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3990.map.gz / Format: CCP4 / Size: 54.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...
Entire | Name: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of a Human AL Patient |
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Components |
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-Supramolecule #1: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...
Supramolecule | Name: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of a Human AL Patient type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 5.00 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 50.0 mM / Component - Name: Tris |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 50 % / Instrument: GATAN CRYOPLUNGE 3 Details: Incubation of 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 |
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Image recording | Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Frames/image: 1-73 / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |