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- PDB-6sdz: transthyritin derived amyloid fibril from patient with hereditary... -

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Basic information

Entry
Database: PDB / ID: 6sdz
Titletransthyritin derived amyloid fibril from patient with hereditary V30M ATTR amyloidosis
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / amyloid fibril / systemic ATTR amyloidosis / ex vivo / misfolding / patient tissue / transthyritin
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
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: 2.97 Å
AuthorsFritz, G. / Agarwal, S. / Faendrich, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSCHM 3276/1 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis.
Authors: Matthias Schmidt / Sebastian Wiese / Volkan Adak / Jonas Engler / Shubhangi Agarwal / Günter Fritz / Per Westermark / Martin Zacharias / Marcus Fändrich /
Abstract: ATTR amyloidosis is one of the worldwide most abundant forms of systemic amyloidosis. The disease is caused by the misfolding of transthyretin protein and the formation of amyloid deposits at ...ATTR amyloidosis is one of the worldwide most abundant forms of systemic amyloidosis. The disease is caused by the misfolding of transthyretin protein and the formation of amyloid deposits at different sites within the body. Here, we present a 2.97 Å cryo electron microscopy structure of a fibril purified from the tissue of a patient with hereditary Val30Met ATTR amyloidosis. The fibril consists of a single protofilament that is formed from an N-terminal and a C-terminal fragment of transthyretin. Our structure provides insights into the mechanism of misfolding and implies the formation of an early fibril state from unfolded transthyretin molecules, which upon proteolysis converts into mature ATTR amyloid fibrils.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
I: Transthyretin
J: Transthyretin
K: Transthyretin


Theoretical massNumber of molelcules
Total (without water)151,90411
Polymers151,90411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area75620 Å2
ΔGint-282 kcal/mol
Surface area28190 Å2
MethodPISA

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Components

#1: Protein
Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13809.426 Da / Num. of mol.: 11 / Mutation: V30M / Source method: isolated from a natural source
Details: transthyritin V30M fragments, residues 11-35 and residues 57-123
Source: (natural) Homo sapiens (human) / References: UniProt: P02766

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Transthyretin derived amyloid fibril (V30M) / Type: COMPLEX / Details: ex vivo ATTR amyloid fibril from human tissue / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7 / Details: Water extract
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 96 %

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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 FIELD / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEMimage acquisition
4GctfCTF correction
7Coot0.9model fitting
11RELIONclassification
12RELION2.13D reconstruction
19PHENIXmodel refinement
20REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.19 ° / Axial rise/subunit: 4.825 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 103663
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70624 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingB value: 89.59 / Protocol: AB INITIO MODEL / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088162
ELECTRON MICROSCOPYf_angle_d0.72711099
ELECTRON MICROSCOPYf_dihedral_angle_d17.1214829
ELECTRON MICROSCOPYf_chiral_restr0.0481298
ELECTRON MICROSCOPYf_plane_restr0.0041375

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