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- PDB-2m5n: Atomic-resolution structure of a cross-beta protofilament -

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Basic information

Entry
Database: PDB / ID: 2m5n
TitleAtomic-resolution structure of a cross-beta protofilament
ComponentsTransthyretin
KeywordsPROTEIN FIBRIL / Amyloid fibril / Cross-beta structure
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)
MethodSOLID-STATE NMR / simulated annealing
Model detailslowest energy, model1
AuthorsFitzpatrick, A.W.P. / Debelouchina, G.T. / Bayro, M.J. / Clare, D.K. / Caporini, M.A. / Bajaj, V.S. / Jaroniec, C.P. / Wang, L. / Ladizhansky, V. / Muller, S. ...Fitzpatrick, A.W.P. / Debelouchina, G.T. / Bayro, M.J. / Clare, D.K. / Caporini, M.A. / Bajaj, V.S. / Jaroniec, C.P. / Wang, L. / Ladizhansky, V. / Muller, S. / MacPhee, C.E. / Waudby, C.A. / Mott, H.R. / de Simone, A. / Knowles, T.P.J. / Saibil, H.R. / Vendruscolo, M. / Orlova, E.V. / Griffin, R.G. / Dobson, C.M.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure and hierarchical assembly of a cross-β amyloid fibril.
Authors: Anthony W P Fitzpatrick / Galia T Debelouchina / Marvin J Bayro / Daniel K Clare / Marc A Caporini / Vikram S Bajaj / Christopher P Jaroniec / Luchun Wang / Vladimir Ladizhansky / Shirley A ...Authors: Anthony W P Fitzpatrick / Galia T Debelouchina / Marvin J Bayro / Daniel K Clare / Marc A Caporini / Vikram S Bajaj / Christopher P Jaroniec / Luchun Wang / Vladimir Ladizhansky / Shirley A Müller / Cait E MacPhee / Christopher A Waudby / Helen R Mott / Alfonso De Simone / Tuomas P J Knowles / Helen R Saibil / Michele Vendruscolo / Elena V Orlova / Robert G Griffin / Christopher M Dobson /
Abstract: The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have ...The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale--including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy--we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils.
History
DepositionFeb 27, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
F: Transthyretin
G: Transthyretin
H: Transthyretin
I: Transthyretin
J: Transthyretin
K: Transthyretin
L: Transthyretin
M: Transthyretin
N: Transthyretin
O: Transthyretin
P: Transthyretin


Theoretical massNumber of molelcules
Total (without water)19,17416
Polymers19,17416
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 1198.366 Da / Num. of mol.: 16 / Fragment: UNP residues 125-135 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02766

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D DQ-DRAWS
121REDOR
131ZF-TEDOR
1412D PDSD

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Sample preparation

DetailsContents: 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115), 10% acetonitrile/water solution
Solvent system: 10% acetonitrile/water solution
SampleConc.: 15 mg/mL / Component: TTR(105-115)-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 2 / Pressure: ambient / Temperature units: K

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NMR measurement

NMR spectrometer
TypeManufacturerField strength (MHz)Spectrometer-ID
Bruker N/ABruker9001
N/A N/A7502
N/A N/A5003

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Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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