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- PDB-9d2g: Cryo-EM structure of amyloid fibril extracted from liver of a var... -

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Basic information

Entry
Database: PDB / ID: 9d2g
TitleCryo-EM structure of amyloid fibril extracted from liver of a variant ATTR T60A amyloidosis patient 3
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / Transthyretin / Amyloidosis / ATTR / liver
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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: 3.1 Å
AuthorsNguyen, A.B. / Fernandez-Ramirez, M.C. / 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: Structure / Year: 2025
Title: Structural and molecular homogeneity of ATTRv-T60A amyloid fibrils across patients and organs
Authors: Fernandez-Ramirez, M.D.C. / Nguyen, B.A. / Afrin, S. / Singh, V. / Evers, B. / Shelton, J.M. / Escobar, C.L. / Bassett, P. / Wang, L. / Pekala, M. / Ahmed, Y. / Cabrera Hernandez, L.O. / ...Authors: Fernandez-Ramirez, M.D.C. / Nguyen, B.A. / Afrin, S. / Singh, V. / Evers, B. / Shelton, J.M. / Escobar, C.L. / Bassett, P. / Wang, L. / Pekala, M. / Ahmed, Y. / Cabrera Hernandez, L.O. / Pedretti, R. / Singh, P. / Canepa, J. / Wosztyl, A. / Li, Y. / Boyer, D.R. / Cao, Q. / Saelices, L.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,7375
Polymers68,7375
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13747.334 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Liver / Tissue: Liver / References: UniProt: P02766
Has protein modificationN

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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: Amyloid fibril from liver of a variant ATTR T60A amyloidosis patient
Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Cellular location: extracellular / Organ: liver / Tissue: liver
Buffer solutionpH: 7
Details: We used water as the buffer for the final elution of fibrils
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 5.93 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6691

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Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selection
2EPU3.5image acquisition
4RELION4CTF correctionCTFFIND-4.1
7Coot0.9.8.1model fitting
9PHENIX1.2model refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.25 ° / Axial rise/subunit: 4.91 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 727422 / Details: particle boxsize of 256 px
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30791 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9d24

9d24


Pdb chain-ID: A / Accession code: 9d24 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033685
ELECTRON MICROSCOPYf_angle_d0.6225015
ELECTRON MICROSCOPYf_dihedral_angle_d6.021495
ELECTRON MICROSCOPYf_chiral_restr0.051590
ELECTRON MICROSCOPYf_plane_restr0.006620

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