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- PDB-2kj3: High-resolution structure of the HET-s(218-289) prion in its amyl... -

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Basic information

Entry
Database: PDB / ID: 2kj3
TitleHigh-resolution structure of the HET-s(218-289) prion in its amyloid form obtained by solid-state NMR
ComponentsSmall s protein
KeywordsPROTEIN FIBRIL / HET-s(218-289) / BETA-SOLENOID / PRION / AMYLOID FIBRIL / PARALLEL BETA-SHEETS / HYDROPHOBIC CORE / SALT BRIDGES / ASPARAGINE LADDERS / BETA-HELIX
Function / homologyHet-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
Function and homology information
Biological speciesPodospora anserina (fungus)
MethodSOLID-STATE NMR / simulated annealing, TORSION ANGLE DYNAMICS
Model detailslowest energy, model 1
AuthorsVan Melckebeke, H. / Wasmer, C. / Lange, A. / AB, E. / Loquet, A. / Meier, B.H.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
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: Journal: Science / Year: 2008
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
DepositionMay 20, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small s protein
B: Small s protein
C: Small s protein


Theoretical massNumber of molelcules
Total (without water)26,0033
Polymers26,0033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8133.4 Å2
ΔGint-19.3 kcal/mol
Surface area11360.9 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy
DetailsTHE 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 Small s protein / HET-s


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.) Podospora anserina (fungus) / Gene: small s / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q03689

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Details: Three consecutive HET-s(218-289) prion proteins in their amyloid conformation.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112PDSD
123PDSD
134PDSD
141PAR
151CHHC
166CHHC
171NHHC
185NHHC
195PAIN
NMR detailsText: THE STUDY HAS BEEN PERFORMED BY SOLID-STATE NMR.

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Sample preparation

Details
Solution-IDContentsSolvent system
1100% [U-100% 13C; U-100% 15N] HET-s(218-289)-1, 100% H2O100% H2O
2100% [U-100% 2-13C; U-100% 15N] HET-s(218-289)-2, 100% H2O100% H2O
340% [U-100% 2-13C; U-100% 15N] HET-s(218-289)-3, 60% unlabelled HET-s(218-289)-4, 100% H2O100% H2O
440% [U-100% 1,3-13C; U-100% 15N] HET-s(218-289)-5, 60% unlabelled HET-s(218-289)-6, 100% H2O100% H2O
550% [U-100% 15N] HET-s(218-289)-7, 50% [U-100% 13C] HET-s(218-289)-8, 100% H2O100% H2O
640% [U-100% 13C; U-100% 15N] HET-s(218-289)-9, 60% unlabelled HET-s(218-289)-10, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 %HET-s(218-289)-1[U-100% 13C; U-100% 15N]1
100 %HET-s(218-289)-2[U-100% 2-13C; U-100% 15N]2
40 %HET-s(218-289)-3[U-100% 2-13C; U-100% 15N]3
60 %HET-s(218-289)-43
40 %HET-s(218-289)-5[U-100% 1,3-13C; U-100% 15N]4
60 %HET-s(218-289)-64
50 %HET-s(218-289)-7[U-100% 15N]5
50 %HET-s(218-289)-8[U-100% 13C]5
40 %HET-s(218-289)-9[U-100% 13C; U-100% 15N]6
60 %HET-s(218-289)-106
Sample conditionsIonic strength: 0 / pH: 7.5 / Pressure: AMBIENT / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE8501
BRUKER AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT, MUMENTHALERstructure calculation
TopSpinBruker Biospinprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PROCHECKNMRLaskowski and MacArthurdata analysis
CARAKeller and Wuthrichpeak picking
XwinNMRBruker Biospinprocessing
CNSrefinement
RefinementMethod: simulated annealing, TORSION ANGLE DYNAMICS / Software ordinal: 1 / Details: CNS water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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