SAXSdb — 3wbm

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

DNA/RNA-binding protein Alba 1

Sulfolobus shibatae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 4 RNA 2	RNA (25-MER) × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALBA1_SULSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 1–97 Author chain B； PDBConstruct 1–97； UniProt 1–97 Author chain C； PDBConstruct 1–97； UniProt 1–97 Author chain D； PDBConstruct 1–97； UniProt 1–97

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	3wbm
Deposition date deposition_date	2013-05-20
Structure title title	Crystal Structure of protein-RNA complex
Keywords keywords	PROTEIN-RNA COMPLEX, DNA/RNA BINDING, RNA BINDING PROTEIN-RNA complex; RNA BINDING 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.

3wbm__assembly_1__model_1

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

Download this curve (.dat)

3wbm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wbm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.95 Å
Rg (electron density)	24.79 Å
Total Rg	25.58 Å
Atom count	3714
Residues	395
Excluded volume	63755 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wbm__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	DNA/RNA-binding protein Alba 1
Molecular weight formula_weight	10601.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4024

MSSGTPTPSNVVLIGKKPVMNYVLAALTLLNQGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQDGRQSRVSTIEIAIRKK

Source Source

Source organism organism	Sulfolobus shibatae
NCBI taxonomy ID ncbi_taxonomy_id	2286
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	RNA (25-MER)
Molecular weight formula_weight	7949.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	X,Y

GGUAAGAGCACCCGACUGCUCUUCC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	310

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3wbma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.6 — AlbA-like
Family Family family	d.68.6.1 — DNA-binding protein AlbA

Domain ID domain_id	d3wbmb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.6 — AlbA-like
Family Family family	d.68.6.1 — DNA-binding protein AlbA

Domain ID domain_id	d3wbmc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.6 — AlbA-like
Family Family family	d.68.6.1 — DNA-binding protein AlbA

Domain ID domain_id	d3wbmd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.6 — AlbA-like
Family Family family	d.68.6.1 — DNA-binding protein AlbA

CATH v4.4 (4 domains)

Domain ID domain_id	3wbmA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

Domain ID domain_id	3wbmB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

Domain ID domain_id	3wbmC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

Domain ID domain_id	3wbmD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	20 — Alba-like domain

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Unit-cell length a length_a	169.890 Å
Unit-cell length b length_b	69.760 Å
Unit-cell length c length_c	48.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	43.804 Å
R factor r_factor	0.2139
R_work r_work	0.2120
R_free r_free	0.2486

Crystal Structure of protein-RNA complex

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

DNA/RNA-binding protein Alba 1

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

3wbm__assembly_1__model_1

3wbm__assembly_1__model_1 | I(q)

3wbm__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of protein-RNA complex

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

DNA/RNA-binding protein Alba 1

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

3wbm__assembly_1__model_1

3wbm__assembly_1__model_1 | I(q)

3wbm__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)