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- EMDB-65409: Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-65409
TitleCryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)
Map data
Sample
  • Complex: Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate
    • Protein or peptide: Probable solanesyl-diphosphate synthase 3, chloroplastic
    • Protein or peptide: Fibrillin protein 5 homolog
  • Ligand: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
  • Ligand: COBALT (II) ION
KeywordsChloroplast / Plastoquinone-9 / Catalysis / TRANSFERASE
Function / homology
Function and homology information


all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific] / plastoquinone biosynthetic process / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / prenyltransferase activity / isoprenoid biosynthetic process / chloroplast / metal ion binding
Similarity search - Function
Plastid lipid-associated protein/fibrillin conserved domain / Plastid-lipid-associated protein / PAP_fibrillin / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Probable solanesyl-diphosphate synthase 3, chloroplastic / Fibrillin protein 5 homolog
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsXiao H / Li M / Yang G-F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate
Authors: Xiao H / Li M / Yang G-F
History
DepositionJul 18, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65409.png

Downloads & links

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Map

FileDownload / File: emd_65409.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 360 pix.
= 249.12 Å		0.69 Å/pix.
x 360 pix.
= 249.12 Å		0.69 Å/pix.
x 360 pix.
= 249.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.692 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.286
Minimum - Maximum-2.0814114 - 3.1658585
Average (Standard dev.)-0.0004188912 (±0.049037877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 249.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65409_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65409_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 : Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in compl...

EntireName: Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate
Components
  • Complex: Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate
    • Protein or peptide: Probable solanesyl-diphosphate synthase 3, chloroplastic
    • Protein or peptide: Fibrillin protein 5 homolog
  • Ligand: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
  • Ligand: COBALT (II) ION

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Supramolecule #1: Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in compl...

SupramoleculeName: Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: Probable solanesyl-diphosphate synthase 3, chloroplastic

MacromoleculeName: Probable solanesyl-diphosphate synthase 3, chloroplastic
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific]
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 35.721609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSVSSLLEVV ADDLLKLNNN LKSLVGAENP VLVSAAEQIF GAGGKRLRPA LVFLVSRATA ELAGLLELTT EHQRLAEIIE MIHTASLIH DDVIDDSGMR RGKETIHQLY GTRVAVLAGD FMFAQSSWFL ANLENIEVIK LISQVIKDFA SGEIKQASTL F DCDITLDD ...String:
MSVSSLLEVV ADDLLKLNNN LKSLVGAENP VLVSAAEQIF GAGGKRLRPA LVFLVSRATA ELAGLLELTT EHQRLAEIIE MIHTASLIH DDVIDDSGMR RGKETIHQLY GTRVAVLAGD FMFAQSSWFL ANLENIEVIK LISQVIKDFA SGEIKQASTL F DCDITLDD YLLKSYYKTA SLIAASTRSA AIFSGVSTAI CEQMYEYGRN LGLSFQVVDD ILDFTQSAEQ LGKPAGSDLA KG NLTAPVI FALQDEPQLR EIIDSEFSET NSLATAIELV HRSGGIKRAH ELAREKGEIA IQSLQCLPRS EFRSTLENMV KYN LERID

UniProtKB: Probable solanesyl-diphosphate synthase 3, chloroplastic

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Macromolecule #2: Fibrillin protein 5 homolog

MacromoleculeName: Fibrillin protein 5 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.165436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EAALGDAKDA LYAALEGMNR GIFGMTSEKR SEIHALVELL ESKNPTPEPT DKLQDKVDGC WRLVYSTISI LGKKRTKLGL RDFISLGDF FQMIDVKEEK AVNVIKFSAR ALKILSGQLT IEASYKITTK TKVDITLDSS TITPDQLMNI FQKNYDMLLA I FNPEGWLE ...String:
EAALGDAKDA LYAALEGMNR GIFGMTSEKR SEIHALVELL ESKNPTPEPT DKLQDKVDGC WRLVYSTISI LGKKRTKLGL RDFISLGDF FQMIDVKEEK AVNVIKFSAR ALKILSGQLT IEASYKITTK TKVDITLDSS TITPDQLMNI FQKNYDMLLA I FNPEGWLE ITYVDESLRI GRDDKANIFV LERADPSEV

UniProtKB: Fibrillin protein 5 homolog

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Macromolecule #3: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetra...

MacromoleculeName: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
type: ligand / ID: 3 / Number of copies: 2 / Formula: GGS
Molecular weightTheoretical: 466.509 Da
Chemical component information

ChemComp-GGS:
phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid

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Macromolecule #4: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 577732
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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