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

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Basic information

Entry
Database: PDB / ID: 4tuw
Titledrosophila stem-loop binding protein complexed with histone mRNA stem-loop, phospho mimic of TPNK and C-terminal region
Components
  • (HISTONE MRNA 3' STEM LOOP) x 2
  • Histone RNA hairpin-binding protein
KeywordsRNA BINDING PROTEIN/RNA / SLBP / histone mRNA stem-loop / phospho mimic / 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 / MOLECULAR REPLACEMENT / Resolution: 2.902 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 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / 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_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Source and taxonomy / Category: entity_src_gen / pdbx_audit_support
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 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: Histone RNA hairpin-binding protein
D: HISTONE MRNA 3' STEM LOOP
C: HISTONE MRNA 3' STEM LOOP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4599
Polymers39,2584
Non-polymers2005
Water00
1
A: Histone RNA hairpin-binding protein
C: HISTONE MRNA 3' STEM LOOP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0555
Polymers19,9342
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-37 kcal/mol
Surface area9110 Å2
MethodPISA
2
B: Histone RNA hairpin-binding protein
D: HISTONE MRNA 3' STEM LOOP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4044
Polymers19,3242
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-26 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.810, 74.810, 161.285
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: 11030.033 Da / Num. of mol.: 2 / Fragment: UNP residues 184-276 / Mutation: T230E, S269E, S271E, S273E, S275E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Slbp, CG11886 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: Q9VAN6
#2: RNA chain HISTONE MRNA 3' STEM LOOP


Mass: 8293.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain HISTONE MRNA 3' STEM LOOP


Mass: 8904.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
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 cacodylate 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 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10448 / % possible obs: 97.6 % / Redundancy: 7.2 % / Rsym value: 0.144 / Net I/σ(I): 13.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 81.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.902→23.733 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 997 9.93 %Random selection
Rwork0.2145 ---
obs0.2194 10039 93.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.902→23.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 1120 5 0 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082435
X-RAY DIFFRACTIONf_angle_d1.1683542
X-RAY DIFFRACTIONf_dihedral_angle_d14.0281090
X-RAY DIFFRACTIONf_chiral_restr0.057426
X-RAY DIFFRACTIONf_plane_restr0.008259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.902-3.05470.40181100.3078989X-RAY DIFFRACTION74
3.0547-3.24560.32411370.25771254X-RAY DIFFRACTION93
3.2456-3.49550.31031420.23311291X-RAY DIFFRACTION96
3.4955-3.84590.27951420.20851325X-RAY DIFFRACTION97
3.8459-4.39930.2291470.21061338X-RAY DIFFRACTION97
4.3993-5.53110.24171540.19561369X-RAY DIFFRACTION99
5.5311-23.73350.23131650.19641476X-RAY DIFFRACTION99

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