SAXSdb — 8tkn

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

Nuclear factor NF-kappa-B p50 subunit

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 4	DNA A × 2 DNA B × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFKB1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 39–350 Author chain B； PDBConstruct 1–312； UniProt 39–350

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	8tkn
Deposition date deposition_date	2023-07-25
Last revision last_revision	2023-10-11
Structure title title	Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 10-mer kappaB DNA from human Neutrophil Gelatinase-associated Lipocalin (NGAL) promoter
Keywords keywords	DNA, NF-kappaB, p50, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

8tkn__assembly_1__model_1

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

Download this curve (.dat)

8tkn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tkn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.69 Å
Rg (electron density)	31.84 Å
Total Rg	32.22 Å
Atom count	5712
Residues	664
Excluded volume	99100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tkn__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	Nuclear factor NF-kappa-B p50 subunit
Molecular weight formula_weight	34924.9 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	5712

GPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVNITKPASVFVQLRRKSDLETSEPKPFLYYPE

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA A
Molecular weight formula_weight	3085.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E

GGGAATGTCC

Entity 3 Entity 3 polymer

Description description	DNA B
Molecular weight formula_weight	3005.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

GGACATTCCC

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Unit-cell length a length_a	67.006 Å
Unit-cell length b length_b	102.644 Å
Unit-cell length c length_c	127.704 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.620 Å
R factor r_factor	0.2413
R_work r_work	0.2388
R_free r_free	0.2878

Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 10-mer kappaB DNA from human Neutrophil Gelatinase-associated Lipocalin (NGAL) promoter

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

Nuclear factor NF-kappa-B p50 subunit

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

8tkn__assembly_1__model_1

8tkn__assembly_1__model_1 | I(q)

8tkn__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 polymer

Polymer Polymer

7. Citations (1)

Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 10-mer kappaB DNA from human Neutrophil Gelatinase-associated Lipocalin (NGAL) promoter

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

Nuclear factor NF-kappa-B p50 subunit

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

8tkn__assembly_1__model_1

8tkn__assembly_1__model_1 | I(q)

8tkn__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 polymer

Polymer Polymer

7. Citations (1)