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- PDB-2kj3: High-resolution structure of the HET-s(218-289) prion in its amyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2kj3 | ||||||
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Title | High-resolution structure of the HET-s(218-289) prion in its amyloid form obtained by solid-state NMR | ||||||
![]() | Small s protein | ||||||
![]() | PROTEIN FIBRIL / HET-s(218-289) / BETA-SOLENOID / PRION / AMYLOID FIBRIL / PARALLEL BETA-SHEETS / HYDROPHOBIC CORE / SALT BRIDGES / ASPARAGINE LADDERS / BETA-HELIX | ||||||
Function / homology | Het-s prion-forming domain / Prion-inhibition and propagation, HeLo domain / HeLo domain superfamily / Het-s 218-289 / Prion-inhibition and propagation / identical protein binding / cytoplasm / Heterokaryon incompatibility protein s![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLID-STATE NMR / simulated annealing, TORSION ANGLE DYNAMICS | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Van Melckebeke, H. / Wasmer, C. / Lange, A. / AB, E. / Loquet, A. / Meier, B.H. | ||||||
![]() | ![]() Title: Atomic-Resolution Three-Dimensional Structure of HET-s(218-289) Amyloid Fibrils by Solid-State NMR Spectroscopy Authors: Van Melckebeke, H. / Wasmer, C. / Lange, A. / AB, E. / Loquet, A. / Bockmann, A. / Meier, B.H. #1: ![]() Title: Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core Authors: Wasmer, C. / Lange, A. / Van Melckebeke, H. / Siemer, A.B. / Riek, R. / Meier, B.H. #2: Journal: Chembiochem / Year: 2009 Title: A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation Authors: Lange, A. / Gattin, Z. / Van Melckebeke, H. / Wasmer, C. / Soragni, A. / van Gunsteren, W.F. / Meier, B.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 383.7 KB | Display | ![]() |
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Full document | ![]() | 757.6 KB | Display | |
Data in XML | ![]() | 81.9 KB | Display | |
Data in CIF | ![]() | 123.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Details | THE RIGID PARTS (I222-A249, T260-W287) OF MOLECULES B AND C CAN BE OBTAINED BY TRANSLATION AND TWIST OF THE RIGID PART OF MOLECULE A. |
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Components
#1: Protein | Mass: 8667.651 Da / Num. of mol.: 3 Fragment: C-TERMINAL PRION FORMING DOMAIN of HET-s, RESIDUES 218-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR Details: Three consecutive HET-s(218-289) prion proteins in their amyloid conformation. | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STUDY HAS BEEN PERFORMED BY SOLID-STATE NMR. |
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Sample preparation
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 7.5 / Pressure: AMBIENT / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, TORSION ANGLE DYNAMICS / Software ordinal: 1 / Details: CNS water refinement | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |