SAXSdb — 5l3v

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

Signal recognition particle 54 kDa protein

Sulfolobus solfataricus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-DIPHOSPHATE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-DIPHOSPHATE × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRP54_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–299； UniProt 1–293 Author chain B； PDBConstruct 7–299； UniProt 1–293

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	5l3v
Deposition date deposition_date	2016-05-24
Structure title title	Structure of the crenarchaeal SRP54 GTPase bound to GDP
Keywords keywords	co-translational protein targeting, Signal Recognition Particle, GTPase, Signaling protein, 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.

5l3v__assembly_1__model_1

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

Download this curve (.dat)

5l3v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5l3v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.50 Å
Rg (electron density)	21.91 Å
Total Rg	22.76 Å
Atom count	2298
Residues	291
Excluded volume	41341 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5l3v__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5l3v__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Signal recognition particle 54 kDa protein
Molecular weight formula_weight	33170.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4777

HHHHHHMLENIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSVLERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQASPIGSVIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILG

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5l3va1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family family	a.24.13.0 — automated matches

Domain ID domain_id	d5l3va2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d5l3vb1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family family	a.24.13.0 — automated matches

Domain ID domain_id	d5l3vb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

CATH v4.4 (4 domains)

Domain ID domain_id	5l3vA01
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	5l3vA02
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	5l3vB01
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	5l3vB02
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	92.168 Å
Unit-cell length b length_b	92.168 Å
Unit-cell length c length_c	148.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	39.136 Å
R factor r_factor	0.1782
R_work r_work	0.1759
R_free r_free	0.2222

Structure of the crenarchaeal SRP54 GTPase bound to GDP

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

Signal recognition particle 54 kDa protein

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

5l3v__assembly_1__model_1

5l3v__assembly_1__model_1 | I(q)

5l3v__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the crenarchaeal SRP54 GTPase bound to GDP

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

Signal recognition particle 54 kDa protein

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

5l3v__assembly_1__model_1

5l3v__assembly_1__model_1 | I(q)

5l3v__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)