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- PDB-4tux: drosophila stem-loop binding protein complexed with histone mRNA ... -

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Basic information

Entry
Database: PDB / ID: 4tux
Titledrosophila stem-loop binding protein complexed with histone mRNA stem-loop
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 hairpin-binding protein RNA-binding domain / 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 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
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 / Resolution: 3.08 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 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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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: Histone RNA hairpin-binding protein
D: RNA (26-MER)
C: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4168
Polymers38,2564
Non-polymers1604
Water00
1
A: Histone RNA hairpin-binding protein
C: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1683
Polymers19,1282
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-22 kcal/mol
Surface area8650 Å2
MethodPISA
2
B: Histone RNA hairpin-binding protein
D: RNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2485
Polymers19,1282
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-33 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.951, 74.951, 173.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 10833.879 Da / Num. of mol.: 2 / 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 #1/H766 (bacteria) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: Q9VAN6
#2: RNA chain RNA (26-MER)


Mass: 8293.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% (wt/vol) PEG 1000, 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2012
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 9127 / % possible obs: 93.4 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 33.7
Reflection shellResolution: 3.08→3.15 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5 / % possible all: 60.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 3.08→37.538 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3172 880 9.95 %
Rwork0.2554 --
obs0.2612 8841 90.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→37.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 1076 4 0 2215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162362
X-RAY DIFFRACTIONf_angle_d1.383431
X-RAY DIFFRACTIONf_dihedral_angle_d12.7731047
X-RAY DIFFRACTIONf_chiral_restr0.065412
X-RAY DIFFRACTIONf_plane_restr0.007250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.27060.4207950.3479847X-RAY DIFFRACTION60
3.2706-3.5230.36931340.33041225X-RAY DIFFRACTION86
3.523-3.87720.34391520.26451400X-RAY DIFFRACTION98
3.8772-4.43740.32031610.25811459X-RAY DIFFRACTION99
4.4374-5.58770.24851620.23861458X-RAY DIFFRACTION99
5.5877-37.54110.32361760.23121572X-RAY DIFFRACTION100

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