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Yorodumi- PDB-3zpk: Atomic-resolution structure of a quadruplet cross-beta amyloid fibril. -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zpk | |||||||||
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Title | Atomic-resolution structure of a quadruplet cross-beta amyloid fibril. | |||||||||
Components | TRANSTHYRETIN | |||||||||
Keywords | PROTEIN FIBRIL / CROSS-BETA STRUCTURE | |||||||||
Function / homology | Function and homology information The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | |||||||||
Method | SOLID-STATE NMR / ELECTRON MICROSCOPY / single particle reconstruction / CNSSOLVE / cryo EM | |||||||||
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.A. ...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.A. / 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3zpk.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zpk.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zpk_validation.pdf.gz | 523.4 KB | Display | wwPDB validaton report |
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Full document | 3zpk_full_validation.pdf.gz | 602.8 KB | Display | |
Data in XML | 3zpk_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3zpk_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/3zpk ftp://data.pdbj.org/pub/pdb/validation_reports/zp/3zpk | HTTPS FTP |
-Related structure data
Related structure data | 2324MC 2323C 5590C 2m5kC 2m5mC 2m5nC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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NMR ensembles |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 114 / Rise per n subunits: 4.67 Å / Rotation per n subunits: -0.89 °) |
-Components
#1: Protein/peptide | Mass: 1198.366 Da / Num. of mol.: 16 / Fragment: RESIDUES 125-135 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P02767 |
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-Experimental details
-Experiment
Experiment |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Quadruplet cross-beta amyloid fibril polymorph / Type: COMPLEX |
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Buffer solution | pH: 2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Holey carbon films R2/2 Quantifoil / Grid type: R2/2 Quantifoil |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Scanner model: ZEISS SCAI |
Radiation wavelength | Relative weight: 1 |
-Processing
3D reconstruction | Num. of particles: 175 / Symmetry type: HELICAL | ||||||||||||
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Refinement | Method to determine structure: CNSSOLVE | ||||||||||||
Refinement step | Cycle: LAST
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NMR ensemble | Conformers submitted total number: 1 |