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Yorodumi- EMDB-26691: Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26691 | |||||||||
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Title | Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient | |||||||||
Map data | Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient | |||||||||
Sample |
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Keywords | Transthyretin / Amyloidosis / Systemic amyloidosis / ATTR / Cardiac / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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: 3.43 Å | |||||||||
Authors | Nguyen BA / Saelices L | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis Authors: Nguyen BA / Singh V / Afrin S / Singh P / Pekala M / Ahmed Y / Pedretti R / Canepa J / Lemoff A / Kluve-Beckerman B / Wydorski PM / Chhapra F / Saelices L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26691.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-26691-v30.xml emd-26691.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26691_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_26691.png | 67.8 KB | ||
Masks | emd_26691_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-26691.cif.gz | 4.9 KB | ||
Others | emd_26691_additional_1.map.gz emd_26691_half_map_1.map.gz emd_26691_half_map_2.map.gz | 3.7 MB 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26691 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26691 | HTTPS FTP |
-Validation report
Summary document | emd_26691_validation.pdf.gz | 1013 KB | Display | EMDB validaton report |
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Full document | emd_26691_full_validation.pdf.gz | 1012.6 KB | Display | |
Data in XML | emd_26691_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_26691_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26691 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26691 | HTTPS FTP |
-Related structure data
Related structure data | 8e7hM M: atomic model generated by this map C: citing same article (ref.) |
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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_26691.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26691_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: postprocessed volume of the main map using the provided mask
File | emd_26691_additional_1.map | ||||||||||||
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Annotation | postprocessed volume of the main map using the provided mask | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_26691_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_26691_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 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MASHRLLLLC LAGLVFVSEA GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHEH AEVVFTANDS GPRRYTIAAL LSPYSYSTTA VVTNPKE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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: 2.1 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |