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- PDB-2rnm: Structure of The HET-s(218-289) prion in its amyloid form obtaine... -

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Basic information

Entry
Database: PDB / ID: 2rnm
TitleStructure 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)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsThe structure of seven HET-s(218-289) prion molecules in their amyloid conformation has been ...The structure of seven HET-s(218-289) prion molecules in their amyloid conformation has been calculated. The 20 lowest energy structures of the five central molecules are provided here, to avoid artefactual border effects.
AuthorsWasmer, C. / Lange, A. / Van Melckebeke, H. / Siemer, A. / Riek, R. / Meier, B.H.
CitationJournal: 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.
History
DepositionJan 24, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2009Group: Version format compliance
Revision 1.2Jun 17, 2015Group: Version format compliance
Revision 1.3Jul 8, 2015Group: Other
Revision 1.4May 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
D: Small s protein
E: Small s protein


Theoretical massNumber of molelcules
Total (without water)43,3385
Polymers43,3385
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Small s protein / HET-s


Mass: 8667.651 Da / Num. of mol.: 5
Fragment: C-terminal prion forming domain, UNP residues 218-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Plasmid: pET-24a / 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: SOLUTION NMR
Details: Solid-State NMR; The structure of seven HET-s(218-289) prion molecules in their amyloid conformation has been calculated. The 20 lowest energy structures of the five central molecules are ...Details: Solid-State NMR; The structure of seven HET-s(218-289) prion molecules in their amyloid conformation has been calculated. The 20 lowest energy structures of the five central molecules are provided here, to avoid artefactual border effects.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CHHC
121NHHC
136CHHC
145NHHC
154PDSD
162PDSD
173PDSD
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); 100% H2O100% H2O
240% [2-13C-100%, 15N-100%] HET-s(218-289); 60% HET-s(218-289); 100% H2O100% H2O
340% [1,3-13C-100%; 15N-100%] HET-s(218-289); 60% HET-s(218-289); 100% H2O100% H2O
4100% [2-13C-100%; 15N-100%] HET-s(218-289); 100% H2O100% H2O
550% [U-100% 13C] HET-s(218-289); 50% [U-100% 15N] HET-s(218-289); 100% H2O100% H2O
640% [U-100% 13C; U-100% 15N] HET-s(218-289); 60% HET-s(218-289); 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 %HET-s(218-289)[U-100% 13C; U-100% 15N]1
40 %HET-s(218-289)[2-13C-100%, 15N-100%]2
40 %HET-s(218-289)[1,3-13C-100%; 15N-100%]3
100 %HET-s(218-289)[2-13C-100%; 15N-100%]4
50 %HET-s(218-289)[U-100% 13C; U-100% 15N]5
40 %HET-s(218-289)[U-100% 13C; U-100% 15N]6
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 AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
PyMOLDeLano Scientific LLCdata analysis
SparkyGoddarddata analysis
CARAKeller and Wuthrichdata analysis
XwinNMRBruker Biospinprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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