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- PDB-2lbu: HADDOCK calculated model of Congo red bound to the HET-s amyloid -

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Basic information

Entry
Database: PDB / ID: 2lbu
TitleHADDOCK calculated model of Congo red bound to the HET-s amyloid
ComponentsSmall s protein
KeywordsPROTEIN FIBRIL / amyloid / ligand / amyloid dye / Congo red / prion protein
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 / Chem-CGO / Heterokaryon incompatibility protein s
Function and homology information
Biological speciesPodospora anserina (fungus)
MethodSOLID-STATE NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsSchutz, A.K. / Soragni, A. / Hornemann, S. / Aguzzi, A. / Ernst, M. / Bockmann, A. / Meier, B.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: The Amyloid-Congo Red Interface at Atomic Resolution.
Authors: Schutz, A.K. / Soragni, A. / Hornemann, S. / Aguzzi, A. / Ernst, M. / Bockmann, A. / Meier, B.H.
History
DepositionApr 7, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0356
Polymers43,3385
Non-polymers6971
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Small s protein


Mass: 8667.651 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 218-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q03689
#2: Chemical ChemComp-CGO / sodium 3,3'-(1E,1'E)-biphenyl-4,4'-diylbis(diazene-2,1-diyl)bis(4-aminonaphthalene-1-sulfonate) / congo red


Mass: 696.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H22N6Na2O6S2

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PDSD
122DREAM

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Sample preparation

Details
Solution-IDContentsSolvent system
115 mg [U-100% 13C; U-100% 15N] HET-s(218-289)-1, 1 mg Congo red-2, waterwater
215 mg [U-100% 13C; U-100% 15N; U-100% 2H] HET-s(218-289)-3, 1 mg Congo red-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mg/mLHET-s(218-289)-1[U-100% 13C; U-100% 15N]1
1 mg/mLCongo red-21
15 mg/mLHET-s(218-289)-3[U-100% 13C; U-100% 15N; U-100% 2H]2
1 mg/mLCongo red-42
Sample conditionsIonic strength: 0 / pH: 7.4 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKAlexandre Bonvinstructure solution
HADDOCKrefinement
RefinementMethod: molecular 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: 4 / Representative conformer: 1

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