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- PDB-8gbr: Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidos... -

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Basic information

Entry
Database: PDB / ID: 8gbr
TitleCardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / Transthyretin / Amyloidosis / Systemic amyloidosis / ATTR / Cardiac
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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
Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNguyen, B.A. / Saelices, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1DP2HL163810-01 United States
American Heart Association847236 United States
CitationJournal: To Be Published
Title: Cardiac amyloid fibrils extracted from a wild-type ATTR amyloidosis patient
Authors: Nguyen, B.A. / Saelices, L.
History
DepositionFeb 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin


Theoretical massNumber of molelcules
Total (without water)79,5255
Polymers79,5255
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 15904.984 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Heart / Plasmid details: Transthyretin amyloidosis / Tissue: CardiacHeart / References: UniProt: P02766

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: cardiac amyloid fibril of wild-type transthyretin amyloidosis
Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Cellular location: extracellular / Organ: Heart / Tissue: Cardiac
Buffer solutionpH: 7 / Details: fibrils are in water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified by water extraction
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2300 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 4.98 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8243

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN22.31particle selection
4RELION3.1CTF correctionCTFFIND-4.1
7Coot0.9.8.1model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX20model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.245 ° / Axial rise/subunit: 4.898 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50584 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 71.63 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Initial fitting was done using Coot with rigid body fit, then real space refinement for better fitting
Atomic model buildingPDB-ID: 8E7D

8e7d


Pdb chain-ID: A / Accession code: 8E7D / Details: Similar structure / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043715
ELECTRON MICROSCOPYf_angle_d0.5485055
ELECTRON MICROSCOPYf_dihedral_angle_d4.971500
ELECTRON MICROSCOPYf_chiral_restr0.05595
ELECTRON MICROSCOPYf_plane_restr0.007625

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