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- PDB-2k8q: NMR Structure of Shq1p N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2k8q
TitleNMR Structure of Shq1p N-terminal domain
ComponentsProtein SHQ1
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / CS domain / Nucleus
Function / homology
Function and homology information


Telomere Extension By Telomerase / box H/ACA snoRNP assembly / unfolded protein binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like ...Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGodin, K.S. / Varani, G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The box H/ACA snoRNP assembly factor Shq1p is a chaperone protein homologous to Hsp90 cochaperones that binds to the Cbf5p enzyme
Authors: Godin, K.S. / Walbott, H. / Leulliot, N. / van Tilbeurgh, H. / Varani, G.
History
DepositionSep 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Protein SHQ1


Theoretical massNumber of molelcules
Total (without water)15,3831
Polymers15,3831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Protein SHQ1 / Small nucleolar RNAs of the box H/ACA family quantitative accumulation protein 1


Mass: 15383.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SHQ1, YIL104C / Production host: Escherichia coli (E. coli) / References: UniProt: P40486

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
21012D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] Shq1 N-terminus, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: Shq1 N-terminus / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 7.0 AMBIENT atm298 K
250 7.0 AMBIENT atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Bruker DMXBrukerDMX7504

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2469 / NOE intraresidue total count: 1332 / NOE medium range total count: 839 / NOE sequential total count: 311 / Hydrogen bond constraints total count: 96 / Protein phi angle constraints total count: 27 / Protein psi angle constraints total count: 27
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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