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- PDB-2fy1: A dual mode of RNA recognition by the RBMY protein -

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Basic information

Entry
Database: PDB / ID: 2fy1
TitleA dual mode of RNA recognition by the RBMY protein
Components
  • RNA-binding motif protein, Y chromosome, family 1 member A1
  • S1A stem-loop RNA
KeywordsSTRUCTURAL PROTEIN/RNA / RNA binding protein / protein-RNA complex / RNA stem-loop / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / RNA splicing / mRNA processing / nuclear speck / ribonucleoprotein complex / mRNA binding / protein-containing complex / RNA binding ...mRNA cis splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / RNA splicing / mRNA processing / nuclear speck / ribonucleoprotein complex / mRNA binding / protein-containing complex / RNA binding / identical protein binding / nucleus
Similarity search - Function
RBM1CTR / RBM1CTR (NUC064) family / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...RBM1CTR / RBM1CTR (NUC064) family / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-binding motif protein, Y chromosome, family 1 member A1 / RNA-binding motif protein, Y chromosome, family 1 member C
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR
AuthorsSkrisovska, L. / Bourgois, C. / Stefl, R. / Kister, L. / Wenter, P. / Elliot, D. / Stevenin, J. / Allain, F.H.T.
CitationJournal: EMBO Rep. / Year: 2007
Title: The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction.
Authors: Skrisovska, L. / Bourgeois, C.F. / Stefl, R. / Grellscheid, S.N. / Kister, L. / Wenter, P. / Elliott, D.J. / Stevenin, J. / Allain, F.H.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
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 / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair_step.tip / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4May 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
B: S1A stem-loop RNA
A: RNA-binding motif protein, Y chromosome, family 1 member A1


Theoretical massNumber of molelcules
Total (without water)19,5252
Polymers19,5252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2070 Å2
ΔGint-4 kcal/mol
Surface area10090 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 30structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: RNA chain S1A stem-loop RNA


Mass: 6711.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was found by in vitro SELEX / Source: (synth.) synthetic construct (others)
#2: Protein RNA-binding motif protein, Y chromosome, family 1 member A1 / RNA-binding motif protein 1 / RRM / RBMY


Mass: 12813.609 Da / Num. of mol.: 1 / Fragment: residues 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15414, UniProt: P0DJD3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D TOCSY
1333D 13C-separated NOESY
1443D 15N-separated NOESY
1552D filtered/edited NOESY
1663D filtered 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM RBMY protein U-15N, 13C; 1mM S1A RNA; 25mM sodium phosphate; 25mM sodium chloride; pH 7; 90% H2O, 10% D2O90% H2O/10% D2O
21mM RBMY protein U-15N; 1mM S1A RNA; 25mM sodium phosphate; 25mM sodium chloride; pH 7; 100% D2O100% D2O
31mM RBMY protein U-15N, 13C; 1mM S1A RNA; 25mM sodium phosphate; 25mM sodium chloride; pH 7; 100% D2O100% D2O
41mM RBMY protein U-15N; 1mM S1A RNA 13C-sugars of the CACAA pentaloop; 25mM sodium phosphate; 25mM sodium chloride; pH 7; 100% D2O100% D2O
51mM RBMY protein U-15N; 1mM S1A RNA 15N, 13C-adenine, cytidine; 25mM sodium phosphate; 25mM sodium chloride; pH 7; 100% D2O100% D2O
61mM RBMY protein U-15N; 1mM S1A RNA 15N, 13C-guanine, uracil; 25mM sodium phosphate; 25mM sodium chloride; pH 7; 100% D2O100% D2O
Sample conditionsIonic strength: 25mM sodium phosphate, 25mM sodium chloride
pH: 7 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX7502
Bruker DRXBrukerDRX6003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Sparky3.106Goddard, TDdata analysis
Amber7refinement
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 17

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