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- PDB-1b7f: SXL-LETHAL PROTEIN/RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b7f
TitleSXL-LETHAL PROTEIN/RNA COMPLEX
Components
  • PROTEIN (SXL-LETHAL PROTEIN)
  • RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsRNA-BINDING PROTEIN/RNA / SPLICING REGULATION / RNP DOMAIN / RNA COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / RNA-BINDING PROTEIN-RNA COMPLEX
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 / pre-mRNA binding / poly(A) binding / positive regulation of smoothened signaling pathway / reciprocal meiotic recombination / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / oogenesis / 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
RNA / RNA (> 10) / Protein sex-lethal
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.6 Å
AuthorsHanda, N. / Nureki, O. / Kurimoto, K. / Kim, I. / Sakamoto, H. / Shimura, Y. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nature / Year: 1999
Title: Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein.
Authors: Handa, N. / Nureki, O. / Kurimoto, K. / Kim, I. / Sakamoto, H. / Shimura, Y. / Muto, Y. / Yokoyama, S.
History
DepositionJan 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Q: RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')
A: PROTEIN (SXL-LETHAL PROTEIN)
B: PROTEIN (SXL-LETHAL PROTEIN)


Theoretical massNumber of molelcules
Total (without water)45,3574
Polymers45,3574
Non-polymers00
Water1,51384
1
P: RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')
A: PROTEIN (SXL-LETHAL PROTEIN)


Theoretical massNumber of molelcules
Total (without water)22,6792
Polymers22,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')
B: PROTEIN (SXL-LETHAL PROTEIN)


Theoretical massNumber of molelcules
Total (without water)22,6792
Polymers22,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.900, 86.800, 160.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99718, 0.04071, 0.06309), (0.06211, 0.0249, -0.99776), (-0.04219, 0.99886, 0.0223)
Vector: -6.10733, 164.80821, 78.86401)

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Components

#1: RNA chain RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3') / TRA PRE-MRNA


Mass: 3707.112 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: ORIGIN OF THE SEQUENCE: DROSOPHILA MELANOGASTER, NUCLEUS
#2: Protein PROTEIN (SXL-LETHAL PROTEIN)


Mass: 18971.578 Da / Num. of mol.: 2 / Fragment: 2 RNP-DOMAINS / Mutation: F166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cellular location: NUCLEUSCell nucleus / Plasmid: PK7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19339
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2NA HEPES11
3LI2SO411
4SPERMINE11
5DIOXANE1,4-Dioxane11
6ZINC ACETATE11
7MGCL211
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-10 mg/mlprotein1drop
210 %PEG60001reservoir
350 mMsodium MOPS1reservoir
4100 mM1reservoirLi2SO4
53 mMspermine1reservoir
61-3 %dioxane1reservoir
72 mMzinc acetate1reservoir
82 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 17053 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rsym value: 0.089 / Net I/σ(I): 12.03
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.73 % / Mean I/σ(I) obs: 1.62 / Rsym value: 0.411 / % possible all: 87.4
Reflection
*PLUS
Num. measured all: 98612 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 87.4 % / Rmerge(I) obs: 0.411

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→15 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.294 -5 %
Rwork0.201 --
obs-16907 98.5 %
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 494 0 84 3236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.482
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.649
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.649

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