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- PDB-9vxi: Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in c... -

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Basic information

Entry
Database: PDB / ID: 9vxi
TitleCryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)
Components
  • Fibrillin protein 5 homolog
  • Probable solanesyl-diphosphate synthase 3, chloroplastic
KeywordsTRANSFERASE / Chloroplast / Plastoquinone-9 / Catalysis
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
: / Chem-GGS / Probable solanesyl-diphosphate synthase 3, chloroplastic / Fibrillin protein 5 homolog
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsXiao, H. / Li, M. / Yang, G.-F.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable solanesyl-diphosphate synthase 3, chloroplastic
B: Fibrillin protein 5 homolog
C: Probable solanesyl-diphosphate synthase 3, chloroplastic
D: Fibrillin protein 5 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,94310
Polymers115,7744
Non-polymers1,1696
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 Probable solanesyl-diphosphate synthase 3, chloroplastic / OsSPS3 / Probable all-trans-nonaprenyl-diphosphate synthase 3 (geranyl-diphosphate specific)


Mass: 35721.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: SPS3, Os12g0271700, LOC_Os12g17320, OsJ_1767i3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0INZ4, all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific]
#2: Protein Fibrillin protein 5 homolog / OsFBN5 / Plastid-lipid-associated protein 7 homolog / chloroplastic


Mass: 22165.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: FBN5, Os04g0422000, LOC_Os04g34460, OsJ_14801, OSJNBa0028I23.21
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0JD85
#3: Chemical ChemComp-GGS / phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid


Mass: 466.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H36O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
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 SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 1800 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.58 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.16_3549model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 577732 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0198296
ELECTRON MICROSCOPYf_angle_d1.04411204
ELECTRON MICROSCOPYf_dihedral_angle_d8.0455072
ELECTRON MICROSCOPYf_chiral_restr0.0711312
ELECTRON MICROSCOPYf_plane_restr0.0051438

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