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- PDB-2mnw: Solution structure of the P22S mutant of N-terminal CS domain of ... -

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Basic information

Entry
Database: PDB / ID: 2mnw
TitleSolution structure of the P22S mutant of N-terminal CS domain of human Shq1
ComponentsProtein SHQ1 homolog
KeywordsPROTEIN BINDING / Dyskerin / Cbf5 / H/ACA
Function / homology
Function and homology information


box H/ACA snoRNP assembly / negative regulation of rRNA processing / positive regulation of telomerase RNA localization to Cajal body / Telomere Extension By Telomerase / protein-RNA complex assembly / unfolded protein binding / positive regulation of apoptotic process / nucleoplasm / cytoplasm / cytosol
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
Protein SHQ1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSingh, M. / Wang, Z. / Cascio, D. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure and Interactions of the CS Domain of Human H/ACA RNP Assembly Protein Shq1.
Authors: Singh, M. / Wang, Z. / Cascio, D. / Feigon, J.
History
DepositionApr 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 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_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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _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: Protein SHQ1 homolog


Theoretical massNumber of molelcules
Total (without water)14,6111
Polymers14,6111
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein SHQ1 homolog


Mass: 14611.280 Da / Num. of mol.: 1 / Fragment: CS domain (UNP residues 1-96) / Mutation: P22S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHQ1 / Plasmid: pET41 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PI26

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HN(CO)CA
1933D (H)CCH-TOCSY
11023D (H)CCH-TOCSY
11123D HBHA(CO)NH
11233D 1H-13C NOESY aliphatic
11323D 1H-15N NOESY
11433D 1H-13C NOESY aromatic
11513D HNHA
11623D HCACO
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data.

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.5-1 mM [U-15N] P22S mutant of human Shq1 CS domain, 95% H2O/5% D2O95% H2O/5% D2O
220 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.5-1 mM [U-99% 13C; U-99% 15N] P22S mutant of human Shq1 CS domain, 95% H2O/5% D2O95% H2O/5% D2O
320 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.5-1 mM [U-99% 13C; U-99% 15N] P22S mutant of human Shq1 CS domain, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMsodium phosphate-11
100 mMsodium chloride-21
1 mMDTT-31
mMP22S mutant of human Shq1 CS domain-4[U-15N]0.5-11
20 mMsodium phosphate-52
100 mMsodium chloride-62
1 mMDTT-72
mMP22S mutant of human Shq1 CS domain-8[U-99% 13C; U-99% 15N]0.5-12
20 mMsodium phosphate-93
100 mMsodium chloride-103
1 mMDTT-113
mMP22S mutant of human Shq1 CS domain-12[U-99% 13C; U-99% 15N]0.5-13
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
XwinNMRBruker Biospindata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2852 / NOE intraresidue total count: 674 / NOE long range total count: 1006 / NOE medium range total count: 329 / NOE sequential total count: 843
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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