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- PDB-2mnj: NMR solution structure of the yeast Pih1 and Tah1 C-terminal doma... -

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Basic information

Entry
Database: PDB / ID: 2mnj
TitleNMR solution structure of the yeast Pih1 and Tah1 C-terminal domains complex
Components
  • Protein interacting with Hsp90 1
  • TPR repeat-containing protein associated with Hsp90
KeywordsPROTEIN BINDING / CS-domain / R2TP / HSP90 / snoRNP assembly
Function / homology
Function and homology information


R2TP complex / box C/D snoRNP assembly / regulation of cell size / RNA splicing / mRNA processing / rRNA processing / protein folding / protein-folding chaperone binding / protein stabilization / ribonucleoprotein complex ...R2TP complex / box C/D snoRNP assembly / regulation of cell size / RNA splicing / mRNA processing / rRNA processing / protein folding / protein-folding chaperone binding / protein stabilization / ribonucleoprotein complex / nucleus / cytoplasm
Similarity search - Function
Immunoglobulin-like - #4160 / Pih1, Ascomycota, CS domain / Fungal Pih1 CS domain / : / PIH1, N-terminal / PIH1 N-terminal domain / : / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats ...Immunoglobulin-like - #4160 / Pih1, Ascomycota, CS domain / Fungal Pih1 CS domain / : / PIH1, N-terminal / PIH1 N-terminal domain / : / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TPR repeat-containing protein associated with Hsp90 / Protein interacting with Hsp90 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsQuinternet, M. / Jacquemin, C. / Charpentier, B. / Manival, X.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure/Function Analysis of Protein-Protein Interactions Developed by the Yeast Pih1 Platform Protein and Its Partners in Box C/D snoRNP Assembly.
Authors: Quinternet, M. / Rothe, B. / Barbier, M. / Bobo, C. / Saliou, J.M. / Jacquemin, C. / Back, R. / Chagot, M.E. / Cianferani, S. / Meyer, P. / Branlant, C. / Charpentier, B. / Manival, X.
History
DepositionApr 8, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR repeat-containing protein associated with Hsp90
B: Protein interacting with Hsp90 1


Theoretical massNumber of molelcules
Total (without water)12,9502
Polymers12,9502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide TPR repeat-containing protein associated with Hsp90 / Tah1


Mass: 2555.813 Da / Num. of mol.: 1 / Fragment: UNP residues 93-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TAH1, YCR060W, YCR60W / Plasmid: pnEA-tah1p93-111 / Production host: Escherichia coli (E. coli) / References: UniProt: P25638
#2: Protein Protein interacting with Hsp90 1 / Pih1 / Nucleolar protein 17


Mass: 10394.039 Da / Num. of mol.: 1 / Fragment: UNP residues 257-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PIH1, NOP17, YHR034C / Plasmid: pnCS-Pih1p257-344 / Production host: Escherichia coli (E. coli) / References: UniProt: P38768

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D 1H-13C NOESY aliphatic
1513D 1H-13C NOESY aromatic
1613D 1H-15N NOESY
1712D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.5 mM [U-99% 13C; U-99% 15N] Tah1, 1.5 mM [U-99% 13C; U-99% 15N] Pih1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMTah1-1[U-99% 13C; U-99% 15N]1
1.5 mMPih1-2[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 50 / pH: 6.4 / Pressure: ambient / Temperature: 298 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSCornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: RECOORD scripts were used
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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