SAXSdb — 3ndb

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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	Signal recognition 54 kDa protein × 1 （Q57565） SRP RNA × 1 PHOSPHATE ION × 1	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 1–87

Signal recognition 54 kDa protein

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	Signal recognition particle 19 kDa protein × 1 （Q58440） SRP RNA × 1 PHOSPHATE ION × 1	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–430； UniProt 3–431

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	3ndb
Deposition date deposition_date	2010-06-07
Structure title title	Crystal structure of a signal sequence bound to the signal recognition particle
Keywords keywords	protein-RNA complex, signal recognition particle, signal sequence, ribonucleoprotein, SIGNALING PROTEIN-RNA complex; SIGNALING PROTEIN/RNA
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.

3ndb__assembly_1__model_1

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

Download this curve (.dat)

3ndb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ndb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.90 Å
Rg (electron density)	40.90 Å
Total Rg	40.98 Å
Atom count	6926
Residues	643
Excluded volume	114190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ndb__assembly_1__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 (4)

Entity 1 Entity 1 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6926

MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN

Source Source

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Signal recognition 54 kDa protein
Molecular weight formula_weight	50014.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGGAMPKELSHLTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLRKGKSGSGGSGSGKLALALLLLLLALAL

Source Source

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Lactococcus lactis

Entity 3 Entity 3 polymer

Description description	SRP RNA
Molecular weight formula_weight	44145.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	M

GUCUCGUCCCGUGGGGCUCGGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCGGCGCUCACGGGGGUGCGGGAC

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3ndbA00
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	3ndbB01
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	3ndbB02
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	3ndbB03
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	108.835 Å
Unit-cell length b length_b	126.275 Å
Unit-cell length c length_c	201.758 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2300
R_work r_work	0.2280
R_free r_free	0.2665

Crystal structure of a signal sequence bound to 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 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

3ndb__assembly_1__model_1

3ndb__assembly_1__model_1 | I(q)

3ndb__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a signal sequence bound to 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 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

3ndb__assembly_1__model_1

3ndb__assembly_1__model_1 | I(q)

3ndb__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)