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- PDB-2mus: HADDOCK calculated model of LIN5001 bound to the HET-s amyloid -

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Basic information

Entry
Database: PDB / ID: 2mus
TitleHADDOCK calculated model of LIN5001 bound to the HET-s amyloid
ComponentsHeterokaryon incompatibility protein s
KeywordsPROTEIN FIBRIL / amyloid fibril / HET-s(218-289) / parallel beta-sheet / beta-solenoid / prion / luminescent conjugated polythiophene
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-3LS / Heterokaryon incompatibility protein s
Function and homology information
Biological speciesPodospora anserina (fungus)
MethodSOLUTION NMR / molecular dynamics
AuthorsHermann, U.S. / Schuetz, A.K. / Shirani, H. / Saban, D. / Nuvolone, M. / Huang, D.H. / Li, B. / Ballmer, B. / Aslund, A.K.O. / Mason, J.J. ...Hermann, U.S. / Schuetz, A.K. / Shirani, H. / Saban, D. / Nuvolone, M. / Huang, D.H. / Li, B. / Ballmer, B. / Aslund, A.K.O. / Mason, J.J. / Rushing, E. / Budka, H. / Hammarstrom, P. / Bockmann, A. / Caflisch, A. / Meier, B.H. / Nilsson, P.K.R. / Hornemann, S. / Aguzzi, A.
Citation
Journal: Sci Transl Med / Year: 2015
Title: Structure-based drug design identifies polythiophenes as antiprion compounds.
Authors: Herrmann, U.S. / Schutz, A.K. / Shirani, H. / Huang, D. / Saban, D. / Nuvolone, M. / Li, B. / Ballmer, B. / Aslund, A.K. / Mason, J.J. / Rushing, E. / Budka, H. / Nystrom, S. / Hammarstrom, ...Authors: Herrmann, U.S. / Schutz, A.K. / Shirani, H. / Huang, D. / Saban, D. / Nuvolone, M. / Li, B. / Ballmer, B. / Aslund, A.K. / Mason, J.J. / Rushing, E. / Budka, H. / Nystrom, S. / Hammarstrom, P. / Bockmann, A. / Caflisch, A. / Meier, B.H. / Nilsson, K.P. / Hornemann, S. / Aguzzi, A.
#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: J.Biomol.Nmr / Year: 2006
Title: 13C, 15N resonance assignment of parts of the HET-s prion protein in its amyloid form.
Authors: Siemer, A.B. / Ritter, C. / Steinmetz, M.O. / Ernst, M. / Riek, R. / Meier, B.H.
History
DepositionSep 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_nmr_sample_details / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_sample_details.contents / _struct_ref_seq_dif.details
Revision 1.3May 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_software / pdbx_nmr_spectrometer / struct_site
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_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

Downloads & links

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Assembly

Deposited unit
A: Heterokaryon incompatibility protein s
B: Heterokaryon incompatibility protein s
C: Heterokaryon incompatibility protein s
D: Heterokaryon incompatibility protein s
E: Heterokaryon incompatibility protein s
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9556
Polymers43,3395
Non-polymers6171
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein
Heterokaryon incompatibility protein s / Small s protein / Vegetative incompatibility protein s


Mass: 8667.717 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) / Gene: het-s, small s / Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03689
#2: Chemical ChemComp-3LS / 3''',4'-bis(carboxymethyl)-2,2':5',2'':5'',2''':5''',2''''-quinquethiophene-5,5''''-dicarboxylic acid


Mass: 616.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H16O8S5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DREAM 4ms
122PDSD 50 ms
NMR detailsText: All experiments were recorded with a rotation at the magic angle

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Sample preparation

Details
Solution-IDContentsSolvent system
115 mg/mL [U-100% 13C; U-100% 15N; U-100% 2H] HET-s(218-289)-1, 100% D2O100% D2O
215 mg/mL [U-10% 13C; U-100% 15N] HET-s(218-289)-2, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mg/mLHET-s(218-289)-1[U-100% 13C; U-100% 15N; U-100% 2H]1
15 mg/mLHET-s(218-289)-2[U-10% 13C; U-100% 15N]2
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
NameDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospindata analysis
TopSpinCCPNprocessing
TopSpinCCPNchemical shift assignment
TopSpinCCPNdata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospindata analysis
TopSpinCCPNprocessing
TopSpinCCPNchemical shift assignment
TopSpinCCPNdata analysis
HADDOCKAlexandre Bonvinstructure solution
HADDOCKAlexandre Bonvingeometry optimization
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 4

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