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- PDB-2mzj: NMR-structure of the Nop6-RBD from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2mzj
TitleNMR-structure of the Nop6-RBD from S. cerevisiae
ComponentsNucleolar protein 6Nucleolus
KeywordsRNA BINDING PROTEIN / RNA binding domain / RBD / RRM
Function / homology
Function and homology information


snoRNA binding / 90S preribosome / rRNA processing / ribosomal small subunit biogenesis / rRNA binding / nucleolus
Similarity search - Function
Nop6, RNA recognition motif / RRM (RNA recognition motif) domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsWurm, J. / Lioutikov, A. / Koetter, P. / Entian, K. / Woehnert, J.
CitationJournal: To be Published
Title: Not known yet
Authors: Wurm, J. / Lioutikov, A. / Koetter, P. / Entian, K. / Woehnert, J.
History
DepositionFeb 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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
Revision 1.2May 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: Nucleolar protein 6


Theoretical massNumber of molelcules
Total (without water)9,2491
Polymers9,2491
Non-polymers00
Water0
1


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

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Components

#1: Protein Nucleolar protein 6 / Nucleolus


Mass: 9248.613 Da / Num. of mol.: 1 / Fragment: Nop6-RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NOP6, YDL213C, D1018 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07623

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR-structure of the Nop6-RBD from S. cerevisiae
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1322D 1H-13C HSQC
1422D 1H-13C HSQC aliphatic
1522D 1H-13C HSQC aromatic
1623D HN(CA)CB
1723D HN(CA)CO
1823D HNCO
1913D 1H-15N NOESY
11023D 1H-13C NOESY aliphatic
11123D 1H-13C NOESY aromatic
11223D H(CCO)NH
11323D HBHA(CO)NH
11423D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] entity, 100 mM sodium chloride, 8 mM sodium phosphate, 2 mM potassium phosphate, 2.7 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] entity, 100 mM sodium chloride, 8 mM sodium phosphate, 2 mM potassium phosphate, 2.7 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-15N]1
100 mMsodium chloride-21
8 mMsodium phosphate-31
2 mMpotassium phosphate-41
2.7 mMpotassium chloride-51
1 mMentity-6[U-13C; U-15N]2
100 mMsodium chloride-72
8 mMsodium phosphate-82
2 mMpotassium phosphate-92
2.7 mMpotassium chloride-102
Sample conditionsIonic strength: 0.13 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
UNIOHerrmannstructure solution
OPALLuginbuhl P, Guntert P, Billeter M, Wuthrich K.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1438 / Hydrogen bond constraints total count: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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