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- EMDB-63769: the complex of D14 and RGSV P3 -

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Basic information

Entry
Database: EMDB / ID: EMD-63769
Titlethe complex of D14 and RGSV P3
Map data
Sample
  • Complex: the complex of D14 and RGSV P3
    • Protein or peptide: Strigolactone esterase D14
    • Protein or peptide: p3
KeywordsDAWRF14 / PLANT PROTEIN
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 subsp. japonica (Japanese rice) / Oryza sativa Japonica Group (Japanese rice) / Tenuivirus oryzabrevis
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsHuang YC
Funding support1 items
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, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63769.png

Downloads & links

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Map

FileDownload / File: emd_63769.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.36
Minimum - Maximum-0.15585956 - 19.800936
Average (Standard dev.)-0.0152177345 (±0.4516574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63769_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63769_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the complex of D14 and RGSV P3

EntireName: the complex of D14 and RGSV P3
Components
  • Complex: the complex of D14 and RGSV P3
    • Protein or peptide: Strigolactone esterase D14
    • Protein or peptide: p3

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Supramolecule #1: the complex of D14 and RGSV P3

SupramoleculeName: the complex of D14 and RGSV P3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

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Macromolecule #1: Strigolactone esterase D14

MacromoleculeName: Strigolactone esterase D14 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 29.519916 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSAKLLQ ILNVRVVGSG ERVVVLSHGF GTDQSAWSRV LPYLTRDHRV VLYDLVCAGS VNPDHFDFRR YDNLDAYVDD LLAILDALR IPRCAFVGHS VSAMIGILAS IRRPDLFAKL VLIGASPRFL NDSDYHGGFE LEEIQQVFDA MGANYSAWAT G YAPLAVGA ...String:
GPLGSAKLLQ ILNVRVVGSG ERVVVLSHGF GTDQSAWSRV LPYLTRDHRV VLYDLVCAGS VNPDHFDFRR YDNLDAYVDD LLAILDALR IPRCAFVGHS VSAMIGILAS IRRPDLFAKL VLIGASPRFL NDSDYHGGFE LEEIQQVFDA MGANYSAWAT G YAPLAVGA DVPAAVQEFS RTLFNMRPDI SLHVCQTVFK TDLRGVLGMV RAPCVVVQTT RDVSVPASVA AYLKAHLGGR TT VEFLQTE GHLPHLSAPS LLAQVLRRAL ARY

UniProtKB: Strigolactone esterase D14

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Macromolecule #2: p3

MacromoleculeName: p3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tenuivirus oryzabrevis
Molecular weightTheoretical: 23.204436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLSSSSSMD IYGNVRPQNW TADDERYMLS LSGLRRFLEY IPHSDRLTVL NWTRHMAAND IQIGALNAFR KKVCDIMYET KDKRINNEL MKLYNELWSK TSSIYNITPC TTCEIYKKEL SQRVPESNIR YETQFIDSRV PIYQFLTPNN VSVVLVQHGN D LPDLNFPR ...String:
MSLSSSSSMD IYGNVRPQNW TADDERYMLS LSGLRRFLEY IPHSDRLTVL NWTRHMAAND IQIGALNAFR KKVCDIMYET KDKRINNEL MKLYNELWSK TSSIYNITPC TTCEIYKKEL SQRVPESNIR YETQFIDSRV PIYQFLTPNN VSVVLVQHGN D LPDLNFPR YVPLGQPRHK IAYYSDSRMI GQFLRIDHH

UniProtKB: p3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 103509
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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