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- PDB-5dv7: Crystal Structure of NF90 tandem dsRBDs with dsRNA -

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Basic information

Entry
Database: PDB / ID: 5dv7
TitleCrystal Structure of NF90 tandem dsRBDs with dsRNA
Components
  • Interleukin enhancer-binding factor 3
  • RNA (5'-R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3')
  • RNA (5'-R(*UP*CP*AP*CP*UP*UP*UP*CP*AP*UP*AP*AP*UP*GP*CP*UP*GP*G)-3')
KeywordsRNA BINDING PROTEIN / double stranded RNA binding domains / dsRM / dsRBDs / dsRNA / NF90 / ILF3 / DRBP76
Function / homology
Function and homology information


Regulation of CDH11 gene transcription / PKR-mediated signaling / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / precatalytic spliceosome / double-stranded RNA binding / virus receptor activity / defense response to virus / single-stranded RNA binding / negative regulation of translation ...Regulation of CDH11 gene transcription / PKR-mediated signaling / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / precatalytic spliceosome / double-stranded RNA binding / virus receptor activity / defense response to virus / single-stranded RNA binding / negative regulation of translation / ribonucleoprotein complex / protein phosphorylation / negative regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Interleukin enhancer-binding factor 3 / : / : / DZF C-terminal domain / DZF domain / DZF N-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Interleukin enhancer-binding factor 3 / : / : / DZF C-terminal domain / DZF domain / DZF N-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Interleukin enhancer-binding factor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJayachandran, U. / Grey, H. / Cook, A.G.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000520/1 United Kingdom
Wellcome Trust092076 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA.
Authors: Jayachandran, U. / Grey, H. / Cook, A.G.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: RNA (5'-R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3')
B: RNA (5'-R(*UP*CP*AP*CP*UP*UP*UP*CP*AP*UP*AP*AP*UP*GP*CP*UP*GP*G)-3')
C: Interleukin enhancer-binding factor 3


Theoretical massNumber of molelcules
Total (without water)87,5253
Polymers87,5253
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-19 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.104, 100.104, 108.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: RNA chain RNA (5'-R(*CP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*AP*AP*AP*GP*UP*GP*A)-3')


Mass: 5780.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*UP*CP*AP*CP*UP*UP*UP*CP*AP*UP*AP*AP*UP*GP*CP*UP*GP*G)-3')


Mass: 5671.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Interleukin enhancer-binding factor 3


Mass: 76072.672 Da / Num. of mol.: 1 / Fragment: UNP residues 17-716
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ilf3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z1X4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 50mM sodium citrate pH 5.0, 1.0M ammonium formate / PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.17 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.17 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 7981 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.1
Reflection shellResolution: 3.5→3.69 Å / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
XDSdata reduction
SCALA3.3.16data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P1X, 2DMY

3p1x

2dmy


Resolution: 3.5→45.413 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 368 4.61 %
Rwork0.2391 --
obs0.2405 7975 99.97 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.147 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0083 Å2-0 Å2-0 Å2
2--4.0083 Å20 Å2
3----8.0166 Å2
Refinement stepCycle: LAST / Resolution: 3.5→45.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 757 0 1 1637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011738
X-RAY DIFFRACTIONf_angle_d1.1152534
X-RAY DIFFRACTIONf_dihedral_angle_d13.418698
X-RAY DIFFRACTIONf_chiral_restr0.066324
X-RAY DIFFRACTIONf_plane_restr0.005202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5003-4.00650.31751260.30092511X-RAY DIFFRACTION100
4.0065-5.04670.26741270.23412505X-RAY DIFFRACTION100
5.0467-45.41650.26331150.22592591X-RAY DIFFRACTION100

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