SAXSdb — 5l3r

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

Signal recognition particle 54 kDa protein, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cell division protein FtsY homolog, chloroplastic × 1 （O80842） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cell division protein FtsY homolog, chloroplastic × 1 （O80842） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SR54C_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–301； UniProt 77–371 Author chain C； PDBConstruct 7–301； UniProt 77–371

Cell division protein FtsY homolog, chloroplastic

Arabidopsis thaliana

UniProt O80842

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Signal recognition particle 54 kDa protein, chloroplastic × 1 （P37107） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Signal recognition particle 54 kDa protein, chloroplastic × 1 （P37107） PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 MAGNESIUM ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CFTSY_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–293； UniProt 80–366 Author chain D； PDBConstruct 7–293； UniProt 80–366

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5l3r
Deposition date deposition_date	2016-05-24
Structure title title	Structure of the GTPase heterodimer of chloroplast SRP54 and FtsY from Arabidopsis thaliana
Keywords keywords	Co-translational protein targeting, Signal Recognition Particle, GTPase, protein transport; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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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.

5l3r__assembly_1__model_1

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

Download this curve (.dat)

5l3r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5l3r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.40 Å
Rg (electron density)	24.60 Å
Total Rg	25.41 Å
Atom count	4262
Residues	557
Excluded volume	76644 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5l3r__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5l3r__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Signal recognition particle 54 kDa protein, chloroplastic
Molecular weight formula_weight	32424.8 kDa
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	8672

HHHHHHMFGQLTGGLEAAWSKLKGEEVLTKDNIAEPMRDIRRALLEADVSLPVVRRFVQSVSDQAVGMGVIRGVKPDQQLVKIVHDELVKLMGGEVSELQFAKSGPTVILLAGLQGVGKTTVCAKLACYLKKQGKSCMLIAGDVYRPAAIDQLVILGEQVGVPVYTAGTDVKPADIAKQGLKEAKKNNVDVVIMDTAGRLQIDKGMMDELKDVKKFLNPTEVLLVVDAMTGQEAAALVTTFNVEIGITGAILTKLDGDSRGGAALSVKEVSGKPIKLVGRGERMEDLEPFYPDRMAGRILG

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cell division protein FtsY homolog, chloroplastic
Molecular weight formula_weight	31733.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

HHHHHHVIDELLLFWNLAETDRVLDELEEALLVSDFGPKITVRIVERLREDIMSGKLKSGSEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLMAAGDTFRAAASDQLEIWAERTGCEIVVAEGDKAKAATVLSKAVKRGKEEGYDVVLCDTSGRLHTNYSLMEELIACKKAVGKIVSGAPNEILLVLDGNTGLNMLPQAREFNEVVGITGLILTKLDGSARGGCVVSVVEELGIPVKFIGVGEAVEDLQPFDPEAFVNAIFS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Molecular weight formula_weight	521.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	140

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5l3rA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5l3rB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	140 — SRP54, nucleotide-binding domain

Domain ID domain_id	5l3rB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5l3rC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5l3rD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	140 — SRP54, nucleotide-binding domain

Domain ID domain_id	5l3rD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	89.790 Å
Unit-cell length b length_b	74.750 Å
Unit-cell length c length_c	107.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	44.886 Å
R factor r_factor	0.1751
R_work r_work	0.1727
R_free r_free	0.2183

Structure of the GTPase heterodimer of chloroplast SRP54 and FtsY from Arabidopsis thaliana

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

Signal recognition particle 54 kDa protein, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Cell division protein FtsY homolog, chloroplastic

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

5l3r__assembly_1__model_1

5l3r__assembly_1__model_1 | I(q)

5l3r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of the GTPase heterodimer of chloroplast SRP54 and FtsY from Arabidopsis thaliana

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

Signal recognition particle 54 kDa protein, 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

Cell division protein FtsY homolog, 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5l3r__assembly_1__model_1

5l3r__assembly_1__model_1 | I(q)

5l3r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)