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

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ID or keywords:

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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(Cambridge,Mass.) / Year: 2026
Title: Editing strigolactone hormone receptor for robust antiviral silencing in rice
Authors: Yang G / Wu M / Zhang S / Huang Y / Liu Y / Yu X / Hu J / Mi L / Gan P / Wu Y / Zou J / Zhang B / Hu Q / Hu J / Yao R / Zhong B / Huang X / Xie H / Ji Y / Li Y / Zhang J / Yan L / Ding SW / Zhao S / Wu J
History
DepositionMar 15, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 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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