SAXSdb — 4xco

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

Signal recognition particle 19 kDa protein

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	RNA × 1 Signal recognition particle 54 kDa protein,signal sequence × 1 （Q57565） MAGNESIUM ION × 8 SODIUM ION × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 1	RNA × 1 Signal recognition particle 54 kDa protein,signal sequence × 1 （Q57565） MAGNESIUM ION × 6 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRP19_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 1–87 Author chain B； PDBConstruct 1–87； UniProt 1–87

Signal recognition particle 54 kDa protein,signal sequence

Methanocaldococcus jannaschii

UniProt Q57565

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	RNA × 1 Signal recognition particle 19 kDa protein × 1 （Q58440） MAGNESIUM ION × 8 SODIUM ION × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 1	RNA × 1 Signal recognition particle 19 kDa protein × 1 （Q58440） MAGNESIUM ION × 6 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRP54_METJA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–149； UniProt 303–451 Author chain D； PDBConstruct 1–149； UniProt 303–451

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	4xco
Deposition date deposition_date	2014-12-18
Structure title title	Signal-sequence induced conformational changes in the signal recognition particle
Keywords keywords	SIGNAL RECOGNITION PARTICLE, SIGNAL SEQUENCE, RECOMBINANT FUSION PROTEIN, RNA STRUCTURE, RNA binding protein; RNA BINDING PROTEIN
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.

4xco__assembly_1__model_1

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

Download this curve (.dat)

4xco__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xco__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.23 Å
Rg (electron density)	26.62 Å
Total Rg	27.12 Å
Atom count	6130
Residues	274
Excluded volume	55755 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xco__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4xco__assembly_2__model_1`	trimeric （3）	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	RNA
Molecular weight formula_weight	31162.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	M,E
Atom count atom_count	13309

GGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCG

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	synthetic construct

Entity 2 Entity 2 polymer

Description description	Signal recognition particle 19 kDa protein
Molecular weight formula_weight	10376.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Signal recognition particle 54 kDa protein,signal sequence
Molecular weight formula_weight	19206.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGGAMPKELSHLTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLRKGKMLRIGGPLGQIMRQLMFKEGSGSGGSGSGKLALALLLLLLALAL

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Lactococcus lactis

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4xcoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.201 — SRP19
Superfamily Superfamily superfamily	d.201.1 — SRP19
Family Family family	d.201.1.1 — SRP19

Domain ID domain_id	d4xcob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.201 — SRP19
Superfamily Superfamily superfamily	d.201.1 — SRP19
Family Family family	d.201.1.1 — SRP19

Domain ID domain_id	d4xcod_
Class class	a — All alpha proteins
Fold Fold fold	a.36 — Signal peptide-binding domain
Superfamily Superfamily superfamily	a.36.1 — Signal peptide-binding domain
Family Family family	a.36.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	4xcoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	30 — Signal recognition particle, SRP19-like subunit

Domain ID domain_id	4xcoB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	30 — Signal recognition particle, SRP19-like subunit

Domain ID domain_id	4xcoD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	30 — Signal recognition particle, SRP54 subunit, M-domain

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Unit-cell length a length_a	91.227 Å
Unit-cell length b length_b	112.971 Å
Unit-cell length c length_c	121.204 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	8

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	48.025 Å
R factor r_factor	0.2112
R_work r_work	0.2089
R_free r_free	0.2576

Signal-sequence induced conformational changes in the signal recognition particle

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

Signal recognition particle 19 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

Signal recognition particle 54 kDa protein,signal sequence

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

4xco__assembly_1__model_1

4xco__assembly_1__model_1 | I(q)

4xco__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Signal-sequence induced conformational changes in the signal recognition particle

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

Signal recognition particle 19 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

Signal recognition particle 54 kDa protein,signal sequence

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

4xco__assembly_1__model_1

4xco__assembly_1__model_1 | I(q)

4xco__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)