9VXI | pdb_00009vxi

Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)

• PDB DOI: https://doi.org/10.2210/pdb9VXI/pdb
• EM Map EMD-65409: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-18 Released: 2025-12-17 
• Deposition Author(s): Xiao, H., Li, M., Yang, G.-F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of SPS3-FBN5 complex from Oryza sativa in complexed with cobalt and geranylgeranyl thiopyrophosphate

Xiao, H., Li, M., Yang, G.-F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 116.94 kDa 
• Atom Count: 8,190 
• Modeled Residue Count: 1,044 
• Deposited Residue Count: 1,044 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable solanesyl-diphosphate synthase 3, chloroplastic	A, C	325	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: SPS3, Os12g0271700, LOC_Os12g17320, OsJ_1767i3 EC: 2.5.1.84
UniProt
Find proteins for Q0INZ4 (Oryza sativa subsp. japonica) Explore Q0INZ4  Go to UniProtKB:  Q0INZ4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrillin protein 5 homolog	B, D	197	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: FBN5, Os04g0422000, LOC_Os04g34460, OsJ_14801, OSJNBa0028I23.21
UniProt
Find proteins for Q0JD85 (Oryza sativa subsp. japonica) Explore Q0JD85  Go to UniProtKB:  Q0JD85

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GGS (Subject of Investigation/LOI)	E [auth A], H [auth C]	phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid C20 H36 O6 P2 S BUSOKXFDTDWPOS-OGGZDJOISA-N
CO	F [auth A], G [auth A], I [auth C], J [auth C]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16_3549
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Xiao, H., Li, M., Yang, G.-F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release