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- PDB-2lbx: Solution structure of the S. cerevisiae H/ACA RNP protein Nhp2p -

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Basic information

Entry
Database: PDB / ID: 2lbx
TitleSolution structure of the S. cerevisiae H/ACA RNP protein Nhp2p
ComponentsH/ACA ribonucleoprotein complex subunit 2
KeywordsRNA BINDING PROTEIN / L7Ae / snoRNP / scaRNP
Function / homology
Function and homology information


box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / rRNA pseudouridine synthesis / snRNA pseudouridine synthesis / box H/ACA snoRNA binding / sno(s)RNA-containing ribonucleoprotein complex / rRNA processing / nucleolus
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
H/ACA ribonucleoprotein complex subunit NHP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKoo, B. / Park, C. / Fernandez, C.F. / Chim, N. / Ding, Y. / Chanfreau, G. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of H/ACA RNP Protein Nhp2p Reveals Cis/Trans Isomerization of a Conserved Proline at the RNA and Nop10 Binding Interface.
Authors: Koo, B.K. / Park, C.J. / Fernandez, C.F. / Chim, N. / Ding, Y. / Chanfreau, G. / Feigon, J.
History
DepositionApr 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.4May 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: H/ACA ribonucleoprotein complex subunit 2


Theoretical massNumber of molelcules
Total (without water)13,2081
Polymers13,2081
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 H/ACA ribonucleoprotein complex subunit 2 / H/ACA snoRNP protein NHP2 / High mobility group-like nuclear protein 2


Mass: 13207.521 Da / Num. of mol.: 1 / Fragment: sequence database residues 36-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NHP2, YDL208W, D1045 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32495

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
1423D HBHA(CO)NH
1513D (H)CCH-TOCSY
1633D 1H-13C NOESY
1723D 1H-15N NOESY
1822D 1H-15N HSQC
1912D 1H-13C HSQC
11013D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM [U-13C; U-15N] HEPES, 200 mM [U-13C; U-15N] potassium chloride, 1 mM [U-13C; U-15N] DTT, 100% D2O100% D2O
220 mM [U-15N] HEPES, 200 mM [U-15N] potassium chloride, 1 mM [U-15N] DTT, 90% H2O/10% D2O90% H2O/10% D2O
320 mM [U-13C; U-15N] HEPES, 200 mM [U-13C; U-15N] potassium chloride, 1 mM [U-13C; U-15N] DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMHEPES-1[U-13C; U-15N]1
200 mMpotassium chloride-2[U-13C; U-15N]1
1 mMDTT-3[U-13C; U-15N]1
20 mMHEPES-4[U-15N]2
200 mMpotassium chloride-5[U-15N]2
1 mMDTT-6[U-15N]2
20 mMHEPES-7[U-13C; U-15N]3
200 mMpotassium chloride-8[U-13C; U-15N]3
1 mMDTT-9[U-13C; U-15N]3
Sample conditionsIonic strength: 0.2 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
XwinNMRBruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 915 / NOE long range total count: 208 / NOE medium range total count: 140 / NOE sequential total count: 567 / Protein phi angle constraints total count: 89 / Protein psi angle constraints total count: 88
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.74 Å / Distance rms dev error: 0.16 Å

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