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Yorodumi- EMDB-29920: Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29920 | |||||||||
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Title | Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient | |||||||||
Map data | Main map | |||||||||
Sample |
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Keywords | Transthyretin / Amyloidosis / Systemic amyloidosis / ATTR / Cardiac / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Nguyen BA / Saelices L | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient Authors: Nguyen BA / Saelices L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29920.map.gz | 49.2 MB | EMDB map data format | |
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Header (meta data) | emd-29920-v30.xml emd-29920.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29920_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_29920.png | 85.6 KB | ||
Filedesc metadata | emd-29920.cif.gz | 5.4 KB | ||
Others | emd_29920_additional_1.map.gz emd_29920_half_map_1.map.gz emd_29920_half_map_2.map.gz | 5.5 MB 49.5 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29920 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29920 | HTTPS FTP |
-Validation report
Summary document | emd_29920_validation.pdf.gz | 774.7 KB | Display | EMDB validaton report |
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Full document | emd_29920_full_validation.pdf.gz | 774.3 KB | Display | |
Data in XML | emd_29920_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_29920_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29920 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29920 | HTTPS FTP |
-Related structure data
Related structure data | 8gbrMC 8e7dC 8e7hC 8g9rC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29920.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.946 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: post-processed map
File | emd_29920_additional_1.map | ||||||||||||
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Annotation | post-processed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 1
File | emd_29920_half_map_1.map | ||||||||||||
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Annotation | half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 2
File | emd_29920_half_map_2.map | ||||||||||||
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Annotation | half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : cardiac amyloid fibril of wild-type transthyretin amyloidosis
Entire | Name: cardiac amyloid fibril of wild-type transthyretin amyloidosis |
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Components |
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-Supramolecule #1: cardiac amyloid fibril of wild-type transthyretin amyloidosis
Supramolecule | Name: cardiac amyloid fibril of wild-type transthyretin amyloidosis type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Heart / Tissue: Cardiac |
-Macromolecule #1: Transthyretin
Macromolecule | Name: Transthyretin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Heart / Tissue: Cardiac |
Molecular weight | Theoretical: 15.904984 KDa |
Sequence | String: MASHRLLLLC LAGLVFVSEA GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIY KVEIDTKSYW KALGISPFHE HAEVVFTAND SGPRRYTIAA LLSPYSYSTT AVVTNPKE UniProtKB: Transthyretin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 / Details: fibrils are in water |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
Details | Purified by water extraction |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8243 / Average exposure time: 4.98 sec. / 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 / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.7 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Similar structure |
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Details | Initial fitting was done using Coot with rigid body fit, then real space refinement for better fitting |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 71.63 / Target criteria: Cross-correlation coefficient |
Output model | PDB-8gbr: |