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- PDB-2n94: NMR structure of yeast Bcd1 protein zinc finger -

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Basic information

Entry
Database: PDB / ID: 2n94
TitleNMR structure of yeast Bcd1 protein zinc finger
ComponentsBox C/D snoRNA protein 1
KeywordsMETAL BINDING PROTEIN / Bcd1 / Zinc Finger
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. / Manival, X.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Functional and Structural Insights of the Zinc-Finger HIT protein family members Involved in Box C/D snoRNP Biogenesis.
Authors: Bragantini, B. / Tiotiu, D. / Rothe, B. / Saliou, J.M. / Marty, H. / Cianferani, S. / Charpentier, B. / Quinternet, M. / Manival, X.
History
DepositionNov 5, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4833
Polymers5,3521
Non-polymers1312
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 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Box C/D snoRNA protein 1


Mass: 5352.312 Da / Num. of mol.: 1 / Fragment: zinc finger domain (UNP residues 1-45)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: BCD1, YHR040W / Plasmid: pnEA-3cH / Production host: Escherichia coli (E. coli) / References: UniProt: P38772
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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 1H-1H NOESY
1212D 1H-15N HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D 1H-1H TOCSY
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D 1H-15N HSQC long range
21512D 1H-1H NOESY
21612D 1H-1H TOCSY
21712D 1H-15N HSQC
21812D 1H-15N HSQC long range
21912D 1H-13C HSQC aliphatic
22012D 1H-13C HSQC aromatic
22113D CBCA(CO)NH
22213D HNCO
22313D HNCA
22413D HN(CA)CB
22513D (H)CCH-TOCSY
22613D 1H-15N NOESY
22713D 1H-13C NOESY aliphatic
22813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM sodium phosphate, 150 mM sodium chloride, 0.5 mM TCEP, 3 mM [U-2H] DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMprotein-1[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate-21
150 mMsodium chloride-31
0.5 mMTCEP-41
3 mMDTT-5[U-2H]1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1160 6.4 ambient 313 K
2160 6.4 ambient 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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