SAXSdb — 9vxi

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable solanesyl-diphosphate synthase 3, chloroplastic

Oryza sativa Japonica Group

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fibrillin protein 5 homolog × 2 （Q0JD85） phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid × 2 COBALT (II) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPS3_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–325； UniProt 91–414 Author chain C； PDBConstruct 2–325； UniProt 91–414

Fibrillin protein 5 homolog

Oryza sativa Japonica Group

UniProt Q0JD85

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Probable solanesyl-diphosphate synthase 3, chloroplastic × 2 （Q0INZ4） phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid × 2 COBALT (II) ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAP7_ORYSJ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–197； UniProt 82–278 Author chain D； PDBConstruct 1–197； UniProt 82–278

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9vxi
Deposition date deposition_date	2025-07-18
Structure title title	Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)
Keywords keywords	Chloroplast; Plastoquinone-9; Catalysis, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9vxi__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9vxi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vxi__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.51 Å
Rg (electron density)	34.95 Å
Total Rg	35.25 Å
Atom count	8190
Residues	1044
Excluded volume	146970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vxi__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Probable solanesyl-diphosphate synthase 3, chloroplastic
Molecular weight formula_weight	35721.6 kDa
EC 编号 ec_number	2.5.1.84
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8190

MSVSSLLEVVADDLLKLNNNLKSLVGAENPVLVSAAEQIFGAGGKRLRPALVFLVSRATAELAGLLELTTEHQRLAEIIEMIHTASLIHDDVIDDSGMRRGKETIHQLYGTRVAVLAGDFMFAQSSWFLANLENIEVIKLISQVIKDFASGEIKQASTLFDCDITLDDYLLKSYYKTASLIAASTRSAAIFSGVSTAICEQMYEYGRNLGLSFQVVDDILDFTQSAEQLGKPAGSDLAKGNLTAPVIFALQDEPQLREIIDSEFSETNSLATAIELVHRSGGIKRAHELAREKGEIAIQSLQCLPRSEFRSTLENMVKYNLERID

Source Source

Source organism organism	Oryza sativa Japonica Group
Common name common_name	Japanese rice
NCBI taxonomy ID ncbi_taxonomy_id	39947
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Fibrillin protein 5 homolog
Molecular weight formula_weight	22165.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

EAALGDAKDALYAALEGMNRGIFGMTSEKRSEIHALVELLESKNPTPEPTDKLQDKVDGCWRLVYSTISILGKKRTKLGLRDFISLGDFFQMIDVKEEKAVNVIKFSARALKILSGQLTIEASYKITTKTKVDITLDSSTITPDQLMNIFQKNYDMLLAIFNPEGWLEITYVDESLRIGRDDKANIFVLERADPSEV

Source Source

Source organism organism	Oryza sativa Japonica Group
Common name common_name	Japanese rice
NCBI taxonomy ID ncbi_taxonomy_id	39947
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
Molecular weight formula_weight	466.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	4

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.47 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	577732

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable solanesyl-diphosphate synthase 3, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Fibrillin protein 5 homolog

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vxi__assembly_1__model_1

9vxi__assembly_1__model_1 | I(q)

9vxi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable solanesyl-diphosphate synthase 3, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fibrillin protein 5 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vxi__assembly_1__model_1

9vxi__assembly_1__model_1 | I(q)

9vxi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)