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- PDB-8igd: The crystal structure of the minimal interaction domains of DRB7.... -

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Basic information

Entry
Database: PDB / ID: 8igd
TitleThe crystal structure of the minimal interaction domains of DRB7.2:DRB4 complex
Components
  • Double-stranded RNA-binding domain (DsRBD)-containing protein
  • Double-stranded RNA-binding protein 4
KeywordsGENE REGULATION / Double stranded RNA Binding proteins (dsRBPs)
Function / homology
Function and homology information


ta-siRNA processing / RNAi-mediated antiviral immune response / miRNA processing / double-stranded RNA binding / defense response to virus / RNA binding / nucleus
Similarity search - Function
double strand RNA binding domain from DEAD END PROTEIN 1 / AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Double-stranded RNA-binding domain (DsRBD)-containing protein / Double-stranded RNA-binding protein 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPaturi, S. / Deshmukh, M.V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP0161 India
CitationJournal: Elife / Year: 2025
Title: The mechanism of DRB7.2:DRB4 mediated sequestering of endogenous inverted-repeat dsRNA precursors in plants
Authors: Paturi, S. / Patra, D. / Behera, P.C. / Aute, R. / Waghela, N. / Kinatukara, P. / Deshmukh, M.V.
History
DepositionFeb 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double-stranded RNA-binding domain (DsRBD)-containing protein
B: Double-stranded RNA-binding domain (DsRBD)-containing protein
C: Double-stranded RNA-binding protein 4
D: Double-stranded RNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)38,5424
Polymers38,5424
Non-polymers00
Water543
1
A: Double-stranded RNA-binding domain (DsRBD)-containing protein
D: Double-stranded RNA-binding protein 4


  • defined by author&software
  • Evidence: NMR relaxation study, The total rotational correlation time of the complex corroborates with that of the heterodimeric complex, isothermal titration calorimetry, DRB7.2M:DRB4D3 interact ...Evidence: NMR relaxation study, The total rotational correlation time of the complex corroborates with that of the heterodimeric complex, isothermal titration calorimetry, DRB7.2M:DRB4D3 interact with 1:1 stoichiometry as reported by ITC studies., NMR titrations
  • 19.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)19,2712
Polymers19,2712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-14 kcal/mol
Surface area8620 Å2
MethodPISA
2
B: Double-stranded RNA-binding domain (DsRBD)-containing protein
C: Double-stranded RNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)19,2712
Polymers19,2712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-12 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.940, 93.940, 102.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Double-stranded RNA-binding domain (DsRBD)-containing protein


Mass: 11002.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4G00420 / Plasmid: pETtrx-1b / Cell line (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -RIPL / References: UniProt: F4JHB3
#2: Protein Double-stranded RNA-binding protein 4 / dsRNA-binding protein 4 / AtDRB4


Mass: 8268.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DBR4 / Plasmid: pET30a / Cell line (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8H1D4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 3 Å3/Da / Density % sol: 59 %
Description: Diamond shaped crystals were formed within 3 days of crystallisation setup.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate tribasic dihydrate, and isopropanol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford cryostream controller 700 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 2019 / Details: VariMax HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.9→29.95 Å / Num. obs: 9938 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 62.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.026 / Rrim(I) all: 0.073 / Net I/σ(I): 22.6
Reflection shellResolution: 2.9→3.04 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.418 / Num. unique obs: 4256 / CC1/2: 0.93 / Rpim(I) all: 0.161 / Rrim(I) all: 0.448 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMv7.2.2data reduction
SCALA3.3.22data scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.95 Å / SU ML: 0.3634 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 462 4.65 %
Rwork0.202 9470 -
obs0.2046 9932 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 0 3 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942125
X-RAY DIFFRACTIONf_angle_d1.0352866
X-RAY DIFFRACTIONf_chiral_restr0.0548313
X-RAY DIFFRACTIONf_plane_restr0.0072356
X-RAY DIFFRACTIONf_dihedral_angle_d6.26231284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.32341510.2533145X-RAY DIFFRACTION100
3-4.180.30011490.21863146X-RAY DIFFRACTION100
4.18-7.120.20891620.17583179X-RAY DIFFRACTION99.82

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