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- PDB-2aqc: NMR Structural analysis of archaeal Nop10 -

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Basic information

Entry
Database: PDB / ID: 2aqc
TitleNMR Structural analysis of archaeal Nop10
ComponentsRibosome biogenesis protein Nop10
KeywordsRNA BINDING PROTEIN / aNop10 / Zinc-Ribbon
Function / homology
Function and homology information


pseudouridine synthesis / snoRNA binding / rRNA processing / ribonucleoprotein complex
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHamma, T. / Reichow, S.L. / Varani, G. / Ferre-D'Amare, A.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
Authors: Hamma, T. / Reichow, S.L. / Varani, G. / Ferre-D'Amare, A.R.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4952
Polymers7,4301
Non-polymers651
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Ribosome biogenesis protein Nop10 /


Mass: 7430.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET 16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys S / References: UniProt: P81303
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1333D 15N-separated NOESY
1443D 13C-separated NOESY
NMR detailsText: Dihedral restraints derived from TALOS predictions. H-bond restraints derived from D20 protection analysis

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM aNop10 unlabelled; Sodium Acetate, KCl, 2mM DTT, 100uM excess ZnCl290% H2O/10% D2O
21mM aNop10 unlabelled; Sodium Acetate, KCl, 2mM DTT, 100uM excess ZnCl2100% D2O
31mM aNop10 15N-labelled; Sodium Acetate, KCl, 2mM DTT, 100uM excess ZnCl290% H2O/10% D2O
41mM aNop10 15N,13C-labelled; Sodium Acetate, KCl, 2mM DTT, 100uM excess ZnCl290% H2O/10% D2O
Sample conditionsIonic strength: 50; 100 / pH: 5.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANAv. 2.0Guntert, P.refinement
NMRPipev. 2.3Delaglio, F.processing
Sparkyv. 3.110Goddard. T.D.data analysis
TALOSv. 2003.027.13.05Cornilescu, G.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1172 restraints, 1048 are NOE-derived distance constraints, 40 dihedral angle restraints,56 distance restraints from hydrogen bonds, 28 distance ...Details: the structures are based on a total of 1172 restraints, 1048 are NOE-derived distance constraints, 40 dihedral angle restraints,56 distance restraints from hydrogen bonds, 28 distance restraints for Zn site geometry
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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