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- PDB-4tv0: Drosophila stem-loop binding protein complexed with histone mRNA ... -

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Basic information

Entry
Database: PDB / ID: 4tv0
TitleDrosophila stem-loop binding protein complexed with histone mRNA stem-loop, Selenomethionine derivative
Components
  • Histone RNA hairpin-binding protein
  • RNA (26-MER)
KeywordsRNA BINDING PROTEIN/RNA / SLBP / histone mRNA stem-loop / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / histone pre-mRNA stem-loop binding / RNA Polymerase II Transcription Termination / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing by stem-loop binding and cleavage / histone pre-mRNA 3'end processing complex / mitotic chromosome condensation / sequence-specific mRNA binding / mRNA transport / RNA stem-loop binding ...SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / histone pre-mRNA stem-loop binding / RNA Polymerase II Transcription Termination / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing by stem-loop binding and cleavage / histone pre-mRNA 3'end processing complex / mitotic chromosome condensation / sequence-specific mRNA binding / mRNA transport / RNA stem-loop binding / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Histone RNA stem-loop-binding protein SLBP1/SLBP2 / Histone RNA hairpin-binding protein, RNA-binding domain / SLBP, RNA-binding domain superfamily / Histone RNA hairpin-binding protein RNA-binding domain
Similarity search - Domain/homology
RNA / RNA (> 10) / Histone RNA hairpin-binding protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsZhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIEHS(T.M.T.H) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation.
Authors: Zhang, J. / Tan, D. / DeRose, E.F. / Perera, L. / Dominski, Z. / Marzluff, W.F. / Tong, L. / Hall, T.M.
History
DepositionJun 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone RNA hairpin-binding protein
B: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3854
Polymers19,3052
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-30 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.929, 103.929, 103.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Histone RNA hairpin-binding protein / Histone stem-loop-binding protein


Mass: 11010.641 Da / Num. of mol.: 1 / Fragment: UNP residues 184-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Slbp, CG11886 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VAN6
#2: RNA chain RNA (26-MER)


Mass: 8293.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% (wt/vol) PEG3350, 0.2 M Ca(Ac)2, 50 mM cacodylic acid, pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 7, 2012
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11133 / % possible obs: 99.8 % / Redundancy: 23.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.601→30.002 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 604 9.97 %
Rwork0.2496 --
obs0.253 11120 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms380 540 2 0 922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007992
X-RAY DIFFRACTIONf_angle_d1.1571454
X-RAY DIFFRACTIONf_dihedral_angle_d14.786462
X-RAY DIFFRACTIONf_chiral_restr0.065179
X-RAY DIFFRACTIONf_plane_restr0.00791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.7190.41941380.3781219X-RAY DIFFRACTION98
2.719-2.86220.3671430.37161254X-RAY DIFFRACTION100
2.8622-3.04140.37651410.3181258X-RAY DIFFRACTION100
3.0414-3.27590.35821370.27621248X-RAY DIFFRACTION100
3.2759-3.60510.2871330.24311261X-RAY DIFFRACTION100
3.6051-4.12560.25841400.20311252X-RAY DIFFRACTION100
4.1256-5.19340.23121440.22421261X-RAY DIFFRACTION100
5.1934-30.00370.27461330.25091258X-RAY DIFFRACTION99

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