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- PDB-9kbz: Cryo-EM structure of DCL4-DRB4CTD-dsRNA complex -

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Basic information

Entry
Database: PDB / ID: 9kbz
TitleCryo-EM structure of DCL4-DRB4CTD-dsRNA complex
Components
  • Dicer-like protein 4
  • Double-stranded RNA-binding protein 4
  • RNA (55-MER)
  • RNA (57-MER)
KeywordsRNA BINDING PROTEIN/RNA / DCL4 / DRB4 / siRNA / Dicer / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


vegetative phase change / lsiRNA processing / polarity specification of adaxial/abaxial axis / RNAi-mediated antiviral immunity against RNA virus / maintenance of shoot apical meristem identity / ta-siRNA processing / RNAi-mediated antiviral immune response / reproductive structure development / miRNA processing / ribonuclease III activity ...vegetative phase change / lsiRNA processing / polarity specification of adaxial/abaxial axis / RNAi-mediated antiviral immunity against RNA virus / maintenance of shoot apical meristem identity / ta-siRNA processing / RNAi-mediated antiviral immune response / reproductive structure development / miRNA processing / ribonuclease III activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / DNA-templated transcription termination / helicase activity / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / defense response to virus / RNA binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / double strand RNA binding domain from DEAD END PROTEIN 1 / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. ...AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / double strand RNA binding domain from DEAD END PROTEIN 1 / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ / PAZ domain profile. / PAZ domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Dicer-like protein 4 / Double-stranded RNA-binding protein 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsWang, C. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325008 China
CitationJournal: To Be Published
Title: Cryo-EM structure of DCL4-DRB4CTD-dsRNA complex
Authors: Wang, C. / Du, J.
History
DepositionOct 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dicer-like protein 4
B: Double-stranded RNA-binding protein 4
C: RNA (57-MER)
D: RNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,4277
Polymers243,3544
Non-polymers733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Dicer-like protein 4


Mass: 193967.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DCL4, At5g20320, F5O24.210 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P84634, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Protein Double-stranded RNA-binding protein 4 / dsRNA-binding protein 4 / AtDRB4


Mass: 13526.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DBR4, At3g62800, F26K9.230 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8H1D4
#3: RNA chain RNA (57-MER)


Mass: 18249.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: GenBank: 20197647
#4: RNA chain RNA (55-MER) / RNA (5'-phosphorylated 55 MER)


Mass: 17610.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: GenBank: 20197647
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of DCL4 in complex with DRB4 CTD and RNA
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.24 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105170 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514349
ELECTRON MICROSCOPYf_angle_d0.58219893
ELECTRON MICROSCOPYf_dihedral_angle_d7.2362795
ELECTRON MICROSCOPYf_chiral_restr0.0372355
ELECTRON MICROSCOPYf_plane_restr0.0052143

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