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- PDB-9mb8: the complex of D14 and RGSV P3 -

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Basic information

Entry
Database: PDB / ID: 9mb8
Titlethe complex of D14 and RGSV P3
Components
  • Strigolactone esterase D14
  • p3
KeywordsPLANT PROTEIN / DAWRF14
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
: / Zinc finger, Tenuivirus / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
p3 / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Tenuivirus oryzabrevis
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsHuang, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2026
Title: Editing strigolactone hormone receptor for robust antiviral silencing in rice.
Authors: Guoyi Yang / Ming Wu / Shuai Zhang / Yucen Huang / Yixiao Liu / Xiyuan Yu / Jiayang Hu / Le Mi / Peng Gan / Yuansheng Wu / Jing Zou / Baogang Zhang / Qun Hu / Jie Hu / Ruifeng Yao / Bojian ...Authors: Guoyi Yang / Ming Wu / Shuai Zhang / Yucen Huang / Yixiao Liu / Xiyuan Yu / Jiayang Hu / Le Mi / Peng Gan / Yuansheng Wu / Jing Zou / Baogang Zhang / Qun Hu / Jie Hu / Ruifeng Yao / Bojian Zhong / Xianbo Huang / Huiting Xie / Yinghua Ji / Yi Li / Jie Zhang / Liming Yan / Shou-Wei Ding / Shanshan Zhao / Jianguo Wu /
Abstract: The small interfering RNA (siRNA) pathway directs broad-spectrum antiviral defense through RNA silencing so that virulent infection requires efficient suppression of the defense mechanism. Here, we ...The small interfering RNA (siRNA) pathway directs broad-spectrum antiviral defense through RNA silencing so that virulent infection requires efficient suppression of the defense mechanism. Here, we show that strigolactone (SL) hormone signaling promotes antiviral silencing in rice plants by transcriptional activation of RNA-dependent RNA polymerase 1 (RDR1) and RDR6. We demonstrate that protein P3 of the rice grassy stunt virus (RGSV) blocks SL signaling by directly sequestering the receptor DWARF14 from DWARF3. Structural and functional analyses of the P3-DWARF14 complex reveal that the aspartic acid at position 102 (D102) of DWARF14 is essential for the P3 interaction but not for SL perception. Notably, a single D102N substitution of DWARF14, introduced into two rice cultivars by cytosine base editing (CBE) confers resistance against RGSV by blocking viral suppression of SL signaling-dependent antiviral silencing. Our findings establish a transgene-free strategy for engineering disease resistance by precise genome editing of the SL receptor to escape pathogen suppression of the endogenous defense pathway.
History
DepositionMar 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Strigolactone esterase D14
C: p3
A: Strigolactone esterase D14
D: p3


Theoretical massNumber of molelcules
Total (without water)105,4494
Polymers105,4494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2


Mass: 29519.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: Escherichia coli (E. coli)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Protein p3


Mass: 23204.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tenuivirus oryzabrevis / Gene: p3v, P3 / Production host: Escherichia coli (E. coli) / References: UniProt: E5AXV2
Has protein modificationY

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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: the complex of D14 and RGSV P3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Oryza sativa subsp. japonica (Japanese rice)39947
21Tenuivirus oryzabrevis3052762
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding 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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103509 / Symmetry type: POINT
RefinementHighest resolution: 3.67 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067270
ELECTRON MICROSCOPYf_angle_d0.8059883
ELECTRON MICROSCOPYf_dihedral_angle_d5.062999
ELECTRON MICROSCOPYf_chiral_restr0.0481114
ELECTRON MICROSCOPYf_plane_restr0.0091275

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