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- PDB-2mjf: Solution structure of the complex between the yeast Rsa1 and Hit1... -

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Basic information

Entry
Database: PDB / ID: 2mjf
TitleSolution structure of the complex between the yeast Rsa1 and Hit1 proteins
Components
  • Protein HIT1
  • Ribosome assembly 1 protein
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


snoRNA localization / pre-snoRNP complex / box C/D snoRNP assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit assembly / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
de novo design (two linked rop proteins) - #260 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1790 / Hit1, C-terminal / Hit1 C-terminal / FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / de novo design (two linked rop proteins) ...de novo design (two linked rop proteins) - #260 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1790 / Hit1, C-terminal / Hit1 C-terminal / FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / de novo design (two linked rop proteins) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein HIT1 / Ribosome assembly 1 protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsQuinternet, M. / Roth, B. / Back, R. / Jacquemin, C. / Manival, X.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Protein Hit1, a novel box C/D snoRNP assembly factor, controls cellular concentration of the scaffolding protein Rsa1 by direct interaction.
Authors: Rothe, B. / Saliou, J.M. / Quinternet, M. / Back, R. / Tiotiu, D. / Jacquemin, C. / Loegler, C. / Schlotter, F. / Pena, V. / Eckert, K. / Morera, S. / Dorsselaer, A.V. / Branlant, C. / ...Authors: Rothe, B. / Saliou, J.M. / Quinternet, M. / Back, R. / Tiotiu, D. / Jacquemin, C. / Loegler, C. / Schlotter, F. / Pena, V. / Eckert, K. / Morera, S. / Dorsselaer, A.V. / Branlant, C. / Massenet, S. / Sanglier-Cianferani, S. / Manival, X. / Charpentier, B.
History
DepositionJan 8, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome assembly 1 protein
B: Protein HIT1


Theoretical massNumber of molelcules
Total (without water)15,4632
Polymers15,4632
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Ribosome assembly 1 protein


Mass: 4543.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RSA1, YPL193W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08932
#2: Protein Protein HIT1


Mass: 10920.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HIT1, YJR055W, J1705 / Production host: Escherichia coli (E. coli) / References: UniProt: P46973

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HN(CA)CO
1913D HNHA
11013D HNHB
11113D (H)CCH-COSY
11213D (H)CCH-TOCSY
11313D C(CO)NH
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic
11713D 1H-15N NOESY
11813D 1H-13C NOESY aliphatic
11913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] rsa, 1 mM [U-100% 13C; U-100% 15N] hit, 150 mM sodium chloride, 90 % H2O, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMrsa-1[U-100% 13C; U-100% 15N]1
1 mMhit-2[U-100% 13C; U-100% 15N]1
150 mMsodium chloride-31
90 %H2O-41
10 %D2O-5[U-100% 2H]1
Sample conditionsIonic strength: 150 / pH: 6.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichstructure solution
CARAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CARAGuntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichstructure solution
CARAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CARAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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