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- PDB-6nz2: NMR solution structure of Bcd1p120-303 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6nz2
TitleNMR solution structure of Bcd1p120-303 from Saccharomyces cerevisiae
ComponentsBox C/D snoRNA protein 1
KeywordsRNA BINDING PROTEIN / snoRNP assembly / RNA binding
Function / homology
Function and homology information


sno(s)RNA metabolic process / snoRNA localization / pre-snoRNP complex / box C/D snoRNP assembly / snoRNA binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / nucleus / metal ion binding / cytoplasm
Similarity search - Function
HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type
Similarity search - Domain/homology
Box C/D snoRNA protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsBragantini, B. / Quinternet, M. / Charpentier, B. / Manival, X.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Nat Commun / Year: 2021
Title: The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity.
Authors: Bragantini, B. / Charron, C. / Bourguet, M. / Paul, A. / Tiotiu, D. / Rothe, B. / Marty, H. / Terral, G. / Hessmann, S. / Decourty, L. / Chagot, M.E. / Strub, J.M. / Massenet, S. / Bertrand, ...Authors: Bragantini, B. / Charron, C. / Bourguet, M. / Paul, A. / Tiotiu, D. / Rothe, B. / Marty, H. / Terral, G. / Hessmann, S. / Decourty, L. / Chagot, M.E. / Strub, J.M. / Massenet, S. / Bertrand, E. / Quinternet, M. / Saveanu, C. / Cianferani, S. / Labialle, S. / Manival, X. / Charpentier, B.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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: Box C/D snoRNA protein 1


Theoretical massNumber of molelcules
Total (without water)21,8641
Polymers21,8641
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11280 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Box C/D snoRNA protein 1


Mass: 21864.262 Da / Num. of mol.: 1 / Fragment: residues 120-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BCD1, YHR040W / Production host: Escherichia coli (E. coli) / References: UniProt: P38772

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D CBCA(CO)NH
161isotropic13D (H)CCH-TOCSY
1201isotropic13D (H)CCH-COSY
1191isotropic13D HNHA
1181isotropic13D 1H-15N NOESY
1171isotropic13D 1H-13C NOESY aliphatic
1161isotropic13D 1H-13C NOESY aromatic
1151isotropic22D 1H-13C HSQC aliphatic
1141isotropic22D 1H-13C HSQC aromatic
1131isotropic22D 1H-15N HSQC
1121isotropic23D 1H-13C NOESY aliphatic
1111isotropic23D 1H-13C NOESY aromatic
1101isotropic23D 1H-15N NOESY
192isotropic13D (H)CCH-TOCSY
182isotropic13D CC(CO)NH
172isotropic12D 1H-13C HSQC aromatic
1272isotropic12D 1H-15N HSQC
1262isotropic13D HNCA
1252isotropic13D HN(CA)CB
1242isotropic13D HN(CA)CO
1232isotropic13D HNCO
1283isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N; U-2H] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O2H_13C_15N_sample90% H2O/10% D2O
filamentous virus31 mM [U-15N] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 12 mg/mL Pf1 phage, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBox C/D snoRNA protein 1[U-13C; U-15N]1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
0.5 mMTCEPnatural abundance1
1 mMBox C/D snoRNA protein 1[U-13C; U-15N; U-2H]2
150 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
0.5 mMTCEPnatural abundance2
1 mMBox C/D snoRNA protein 1[U-15N]3
150 mMsodium chloridenatural abundance3
10 mMsodium phosphatenatural abundance3
0.5 mMTCEPnatural abundance3
12 mg/mLPf1 phagenatural abundance3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxstructure calculation
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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