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- PDB-9vty: Cryo-EM structure of ThS-bound ATTRA97S amyloid fibrils extracted... -

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Basic information

Entry
Database: PDB / ID: 9vty
TitleCryo-EM structure of ThS-bound ATTRA97S amyloid fibrils extracted from patient-derived abdominal adipose biopsy tissue.
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / amyloid / protein fibril.
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / phototransduction, visible light / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / phototransduction, visible light / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / : / 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: 3.3 Å
AuthorsMa, B.Y. / Yao, Y.X. / Li, D. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of ThS-bound ATTRA97S amyloid fibrils extracted from patient-derived abdominal adipose biopsy tissue
Authors: Ma, B.Y. / Yao, Y.X. / Li, D. / Liu, C.
History
DepositionJul 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Transthyretin
B: Transthyretin
N: Transthyretin
F: Transthyretin
K: Transthyretin
H: Transthyretin
D: Transthyretin
R: Transthyretin
L: Transthyretin
I: Transthyretin
E: Transthyretin
G: Transthyretin
S: Transthyretin
J: Transthyretin
P: Transthyretin
A: Transthyretin
C: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,55723
Polymers234,48717
Non-polymers3,0706
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13793.360 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical
ChemComp-A1ETV / 2-[2-[4-(dimethylamino)phenyl]-3-methyl-1,3-benzothiazol-3-ium-6-yl]-3,6-dimethyl-1,3-benzothiazol-3-ium-7-sulfonic acid


Mass: 511.679 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H25N3O3S3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Transthyretin amyloid / Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.3 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58292 / Symmetry type: HELICAL

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