SAXSdb — 3dm5

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

Signal recognition 54 kDa protein

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 22 ACETATE ION × 4 GUANOSINE-5'-DIPHOSPHATE × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 12 ACETATE ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 10 ACETATE ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 6 ACETATE ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 ACETATE ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRP54_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–443； UniProt 1–443 Author chain B； PDBConstruct 1–443； UniProt 1–443

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	3dm5
Deposition date deposition_date	2008-06-30
Structure title title	Structures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.
Keywords keywords	;protein-RNA, Signal Recognition Particle, SRP-GTPase, Protein Targeting, Cytoplasm, GTP-binding, Nucleotide-binding, Ribonucleoprotein, RNA-binding, RNA BINDING PROTEIN, Transport protein ;; RNA BINDING PROTEIN, Transport 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.

3dm5__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dm5__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dm5__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	32.10 Å
Rg (electron density)	32.14 Å
Total Rg	32.40 Å
Atom count	3242
Residues	413
Excluded volume	58189 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dm5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dm5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dm5__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dm5__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dm5__assembly_5__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 (5)

Entity 1 Entity 1 polymer

Description description	Signal recognition 54 kDa protein
Molecular weight formula_weight	49960.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6649

MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRALEEKPPAGISKKEHIIKIVYEELTKFLGTEAKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRMIPGLGYSLPDDVISIGEERLKKFKVIMDSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQMKKLFKSMNKRQLSRLARRFGM

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3dm5A01
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	3dm5A02
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	3dm5A03
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

Domain ID domain_id	3dm5B01
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	3dm5B02
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	3dm5B03
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	127.009 Å
Unit-cell length b length_b	127.009 Å
Unit-cell length c length_c	186.836 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	16

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	64.740 Å
R factor r_factor	0.2230
R_work r_work	0.2220
R_free r_free	0.2590

Structures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.

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

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

3dm5__assembly_5__model_1

3dm5__assembly_5__model_1 | I(q)

3dm5__assembly_5__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.

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

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

3dm5__assembly_5__model_1

3dm5__assembly_5__model_1 | I(q)

3dm5__assembly_5__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)