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- PDB-2sxl: SEX-LETHAL RBD1, NMR, MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 2sxl
TitleSEX-LETHAL RBD1, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsSEX-LETHAL PROTEIN
KeywordsRNA-BINDING DOMAIN / ALTERNATIVE SPLICING / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / sex-chromosome dosage compensation / regulation of stem cell division ...sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / sex-chromosome dosage compensation / regulation of stem cell division / sex determination / poly-pyrimidine tract binding / messenger ribonucleoprotein complex / sex differentiation / alternative mRNA splicing, via spliceosome / negative regulation of receptor signaling pathway via JAK-STAT / poly(A) binding / pre-mRNA binding / positive regulation of smoothened signaling pathway / reciprocal meiotic recombination / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / oogenesis / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / mRNA 3'-UTR binding / mRNA 5'-UTR binding / negative regulation of translation / protein stabilization / molecular adaptor activity / ribonucleoprotein complex / protein-containing complex / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / 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 ...Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING METHOD
AuthorsInoue, M. / Muto, Y. / Sakamoto, H. / Kigawa, T. / Takio, K. / Shimura, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: A characteristic arrangement of aromatic amino acid residues in the solution structure of the amino-terminal RNA-binding domain of Drosophila sex-lethal.
Authors: Inoue, M. / Muto, Y. / Sakamoto, H. / Kigawa, T. / Takio, K. / Shimura, Y. / Yokoyama, S.
#1: Journal: Nature / Year: 1994
Title: Crystal Structure at 1.92 A Resolution of the RNA-Binding Domain of the U1A Spliceosomal Protein Complexed with an RNA Hairpin
Authors: Oubridge, C. / Ito, N. / Evans, P.R. / Teo, C.H. / Nagai, K.
#2: Journal: Biochemistry / Year: 1994
Title: Resonance Assignments and Solution Structure of the Second RNA-Binding Domain of Sex-Lethal Determined by Multidimensional Heteronuclear Magnetic Resonance
Authors: Lee, A.L. / Kanaar, R. / Rio, D.C. / Wemmer, D.E.
#3: Journal: Biochemistry / Year: 1994
Title: Determination of the Secondary Structure and Folding Topology of an RNA Binding Domain of Mammalian Hnrnp A1 Protein Using Three-Dimensional Heteronuclear Magnetic Resonance Spectroscopy
Authors: Garrett, D.S. / Lodi, P.J. / Shamoo, Y. / Williams, K.R. / Clore, G.M. / Gronenborn, A.M.
#4: Journal: Biochemistry / Year: 1992
Title: 1H, 13C, and 15N NMR Assignments and Global Folding Pattern of the RNA-Binding Domain of the Human Hnrnp C Proteins
Authors: Wittekind, M. / Gorlach, M. / Friedrichs, M. / Dreyfuss, G. / Mueller, L.
#5: Journal: Nature / Year: 1990
Title: Crystal Structure of the RNA-Binding Domain of the U1 Small Nuclear Ribonucleoprotein A
Authors: Nagai, K. / Oubridge, C. / Jessen, T.H. / Li, J. / Evans, P.R.
History
DepositionJul 16, 1997Processing site: BNL
Revision 1.0Jul 22, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEX-LETHAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,0621
Polymers10,0621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200SMALLEST RESIDUAL ENERGY
Representative

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Components

#1: Protein SEX-LETHAL PROTEIN


Mass: 10061.507 Da / Num. of mol.: 1 / Fragment: RNA-BINDING DOMAIN 1 (RBD1), RESIDUES 122 - 209 / Mutation: F166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line: BL21 / Gene: SEX-LETHAL / Organ: FRUIT / Plasmid: PK7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19339

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131ROESY
141DQF-COSY
1511H-15N 2D HSQC
1611H-15N 2D HMQC-J
17115N-EDITED NOESY-HSQC

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Sample preparation

Sample conditionspH: 4.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING METHOD
Software ordinal: 1
Details: REFINEMENT WAS DONE USING THE HYBRID DISTANCE GEOMETRY/SIMULATED ANNEALING METHOD (NILGES, M., CLORE, G.M., & GRONENBORN, A.M. (1988) FEBS LETT 229, 317-324) AS CONTAINED IN X-PLOR PROGRAM ...Details: REFINEMENT WAS DONE USING THE HYBRID DISTANCE GEOMETRY/SIMULATED ANNEALING METHOD (NILGES, M., CLORE, G.M., & GRONENBORN, A.M. (1988) FEBS LETT 229, 317-324) AS CONTAINED IN X-PLOR PROGRAM VERSION 3.1 (BRUNGER, 1992). THE RMSD FOR THE BACKBONE COORDINATES OF THE 20 STRUCTURES ACCEPTED AFTER THE LAST ROUND OF REFINEMENT COMPARED TO THE AVERAGE COORDINATES WAS 0.86 (FOR RESIDUES INVOLVED IN SECONDARY STRUCTURE).
NMR ensembleConformer selection criteria: SMALLEST RESIDUAL ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 1

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