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- PDB-6htu: Structure of hStau1 dsRBD3-4 in complex with ARF1 RNA -

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Basic information

Entry
Database: PDB / ID: 6htu
TitleStructure of hStau1 dsRBD3-4 in complex with ARF1 RNA
Components
  • (RNA (19-MER)) x 2
  • Double-stranded RNA-binding protein Staufen homolog 1
KeywordsRNA BINDING PROTEIN / dsRBD / RNA localization / SMD
Function / homology
Function and homology information


lncRNA-mediated post-transcriptional gene silencing / : / anterograde dendritic transport of messenger ribonucleoprotein complex / modification of postsynaptic structure / intracellular mRNA localization / protein localization to synapse / protein phosphatase 1 binding / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development ...lncRNA-mediated post-transcriptional gene silencing / : / anterograde dendritic transport of messenger ribonucleoprotein complex / modification of postsynaptic structure / intracellular mRNA localization / protein localization to synapse / protein phosphatase 1 binding / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development / positive regulation of viral genome replication / rough endoplasmic reticulum / dendrite cytoplasm / positive regulation of long-term synaptic potentiation / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / double-stranded RNA binding / cellular response to oxidative stress / cell body / neuron projection / mRNA binding / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / : / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain ...Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / : / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Double-stranded RNA-binding protein Staufen homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.888 Å
AuthorsEmmerich, C. / Lazzaretti, D. / Bandholz-Cajamarca, L. / Bono, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council310957 Germany
German Research FoundationBO3588/2-1 Germany
CitationJournal: Life Sci Alliance / Year: 2018
Title: The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity.
Authors: Lazzaretti, D. / Bandholz-Cajamarca, L. / Emmerich, C. / Schaaf, K. / Basquin, C. / Irion, U. / Bono, F.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _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
D: RNA (19-MER)
F: RNA (19-MER)
A: Double-stranded RNA-binding protein Staufen homolog 1
B: Double-stranded RNA-binding protein Staufen homolog 1
C: Double-stranded RNA-binding protein Staufen homolog 1


Theoretical massNumber of molelcules
Total (without water)73,3885
Polymers73,3885
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-52 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.886, 105.886, 169.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain RNA (19-MER)


Mass: 6092.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain RNA (19-MER)


Mass: 6071.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Double-stranded RNA-binding protein Staufen homolog 1


Mass: 20407.844 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAU1, STAU / Production host: Escherichia coli (E. coli) / References: UniProt: O95793
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM MgCl2, 120 mM KCl, 50 mM Sodium cacodylate pH 6.33, 5% 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.045 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.888→50 Å / Num. obs: 41096 / % possible obs: 99.4 % / Redundancy: 27.5 % / Net I/σ(I): 20.52
Reflection shellResolution: 2.888→3.06 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.888→47.354 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.48
RfactorNum. reflection% reflection
Rfree0.2396 2052 5.02 %
Rwork0.2172 --
obs0.218 40877 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.888→47.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 804 0 3 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032436
X-RAY DIFFRACTIONf_angle_d0.5653475
X-RAY DIFFRACTIONf_dihedral_angle_d10.7861395
X-RAY DIFFRACTIONf_chiral_restr0.036434
X-RAY DIFFRACTIONf_plane_restr0.005311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8875-2.95470.48681260.45872392X-RAY DIFFRACTION92
2.9547-3.02850.40051410.37072569X-RAY DIFFRACTION98
3.0285-3.11040.38311420.30282589X-RAY DIFFRACTION100
3.1104-3.20190.31911350.28962586X-RAY DIFFRACTION99
3.2019-3.30520.28381280.28392585X-RAY DIFFRACTION98
3.3052-3.42330.29671320.27192609X-RAY DIFFRACTION100
3.4233-3.56040.30621320.23762615X-RAY DIFFRACTION100
3.5604-3.72230.19311400.22572609X-RAY DIFFRACTION100
3.7223-3.91850.26351410.20862605X-RAY DIFFRACTION100
3.9185-4.16390.20511390.18952606X-RAY DIFFRACTION100
4.1639-4.48510.18341380.18572612X-RAY DIFFRACTION100
4.4851-4.93610.24771390.1942614X-RAY DIFFRACTION100
4.9361-5.64930.19391370.19352613X-RAY DIFFRACTION100
5.6493-7.11370.27921380.23092625X-RAY DIFFRACTION100
7.1137-47.360.21211440.18872596X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 33.767 Å / Origin y: 103.7219 Å / Origin z: 17.6297 Å
111213212223313233
T0.7082 Å20.0079 Å20.0726 Å2-0.4187 Å20.0685 Å2--0.5198 Å2
L0.3932 °20.1909 °2-0.1447 °2-0.0131 °2-0.7992 °2--0.7771 °2
S-0.0279 Å °-0.1014 Å °0.0568 Å °-0.065 Å °-0.1409 Å °-0.5587 Å °0.0688 Å °-0.0176 Å °-0.0135 Å °
Refinement TLS groupSelection details: all

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