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- PDB-9urh: Structural insight into DNA recognition by RRM1+2 domain of human... -

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Basic information

Entry
Database: PDB / ID: 9urh
TitleStructural insight into DNA recognition by RRM1+2 domain of human ETR-3 protein
Components
  • CUGBP Elav-like family member 2
  • DNA (5'-D(P*TP*GP*GP*TP*C)-3')
KeywordsRNA BINDING PROTEIN / Transcription Factor / Protein DNA complex / Human ETR3 / Dual DNA and RNA binding / RRM
Function / homology
Function and homology information


mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of alternative mRNA splicing, via spliceosome / regulation of heart contraction / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding ...mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of alternative mRNA splicing, via spliceosome / regulation of heart contraction / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / CUGBP Elav-like family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPatra, A. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentICGEB New Delhi Core funds India
CitationJournal: To Be Published
Title: Structural insight into DNA recognition by RRM1+2 domain of human ETR-3 protein
Authors: Patra, A. / Bhavesh, N.S.
History
DepositionApr 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CUGBP Elav-like family member 2
B: DNA (5'-D(P*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0383
Polymers22,0132
Non-polymers241
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, HSQC titration study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-11 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.116, 70.770, 134.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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Components

#1: Protein CUGBP Elav-like family member 2 / CELF-2 / Bruno-like protein 3 / CUG triplet repeat RNA-binding protein 2 / CUG-BP2 / CUG-BP- and ...CELF-2 / Bruno-like protein 3 / CUG triplet repeat RNA-binding protein 2 / CUG-BP2 / CUG-BP- and ETR-3-like factor 2 / ELAV-type RNA-binding protein 3 / ETR-3 / Neuroblastoma apoptosis-related RNA-binding protein / hNAPOR / RNA-binding protein BRUNOL-3


Mass: 20213.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CELF2, BRUNOL3, CUGBP2, ETR3, NAPOR / Production host: Escherichia coli (E. coli) / References: UniProt: O95319
#2: DNA chain DNA (5'-D(P*TP*GP*GP*TP*C)-3')


Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CGT repeats / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.82→37.774 Å / Num. obs: 19591 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.3
Reflection shellResolution: 1.823→1.854 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.172 / Num. unique obs: 965 / CC1/2: 0.787 / Rpim(I) all: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LMZ

4lmz


Resolution: 1.82→37.77 Å / SU ML: 0.2247 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 948 4.84 %
Rwork0.197 18639 -
obs0.1981 19587 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.21 Å2
Refinement stepCycle: LAST / Resolution: 1.82→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 104 1 107 1601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681533
X-RAY DIFFRACTIONf_angle_d0.83822084
X-RAY DIFFRACTIONf_chiral_restr0.061223
X-RAY DIFFRACTIONf_plane_restr0.0089257
X-RAY DIFFRACTIONf_dihedral_angle_d18.5752594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.920.32211550.26472605X-RAY DIFFRACTION99.96
1.92-2.040.2661510.22742604X-RAY DIFFRACTION99.96
2.04-2.20.24311200.21922643X-RAY DIFFRACTION100
2.2-2.420.24661320.22022633X-RAY DIFFRACTION99.89
2.42-2.770.30741310.22792650X-RAY DIFFRACTION99.89
2.77-3.480.21841310.21352702X-RAY DIFFRACTION100
3.49-37.770.171280.16212802X-RAY DIFFRACTION99.32

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