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Open data
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Basic information
Entry | Database: PDB / ID: 2m5n | ||||||
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Title | Atomic-resolution structure of a cross-beta protofilament | ||||||
![]() | Transthyretin | ||||||
![]() | PROTEIN FIBRIL / Amyloid fibril / Cross-beta structure | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
![]() | 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. ...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. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 884.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 611.2 KB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 129.2 KB | Display | |
Data in CIF | ![]() | 128 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2323C ![]() 2324C ![]() 5590C ![]() 2m5kC ![]() 2m5mC ![]() 3zpkC C: citing same article ( |
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Similar structure data | |
Other databases |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 1198.366 Da / Num. of mol.: 16 / Fragment: UNP residues 125-135 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115), 10% acetonitrile/water solution Solvent system: 10% acetonitrile/water solution |
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Sample | Conc.: 15 mg/mL / Component: TTR(105-115)-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | pH: 2 / Pressure: ambient / Temperature units: K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |