+Open data
-Basic information
Entry | Database: PDB / ID: 2m5n | ||||||
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Title | Atomic-resolution structure of a cross-beta protofilament | ||||||
Components | Transthyretin | ||||||
Keywords | PROTEIN FIBRIL / Amyloid fibril / Cross-beta structure | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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 | Homo sapiens (human) | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | 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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m5n.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2m5n.ent.gz | 884.1 KB | Display | PDB format |
PDBx/mmJSON format | 2m5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/2m5n ftp://data.pdbj.org/pub/pdb/validation_reports/m5/2m5n | HTTPS FTP |
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-Related structure data
Related structure data | 2323C 2324C 5590C 2m5kC 2m5mC 3zpkC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / References: UniProt: P02766 |
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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 |