SAXSdb — 3brv

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

Inhibitor of nuclear factor kappa-B kinase subunit beta

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	NF-kappa-B essential modulator × 2 （Q9Y6K9） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NF-kappa-B essential modulator × 1 （Q9Y6K9） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	NF-kappa-B essential modulator × 1 （Q9Y6K9） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	NF-kappa-B essential modulator × 1 （Q9Y6K9） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	NF-kappa-B essential modulator × 1 （Q9Y6K9） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IKKB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–48； UniProt 701–745 Author chain C； PDBConstruct 4–47； UniProt 701–745

NF-kappa-B essential modulator

Homo sapiens

UniProt Q9Y6K9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Inhibitor of nuclear factor kappa-B kinase subunit beta × 2 （O14920） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEMO_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–70； UniProt 44–111 Author chain D； PDBConstruct 3–70； UniProt 44–111

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	3brv
Deposition date deposition_date	2007-12-21
Structure title title	NEMO/IKKb association domain structure
Keywords keywords	;NEMO, IKK-gamma, FIP3, IKKAP1, NF-kB essential modulator, ATP-binding, Kinase, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transferase, Disease mutation, Ectodermal dysplasia, Host-virus interaction, Nucleus, Transcription, Transcription regulation, TRANSFERASE-TRANSCRIPTION COMPLEX ;; TRANSFERASE/TRANSCRIPTION
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.

3brv__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3brv__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3brv__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	23.99 Å
Rg (electron density)	24.89 Å
Total Rg	24.99 Å
Atom count	812
Residues	104
Excluded volume	14279 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3brv__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3brv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3brv__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3brv__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3brv__assembly_5__model_1`	dimeric （2）	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	Inhibitor of nuclear factor kappa-B kinase subunit beta
Molecular weight formula_weight	5437.0 kDa
EC 编号 ec_number	2.7.11.10
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1724

AMAPAKKSEELVAEAHNLCTLLENAIQDTVREQDQSFTALDWSWLQTE

Entity 2 Entity 2 polymer

Description description	NF-kappa-B essential modulator
Molecular weight formula_weight	8533.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MWEQGAPETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3brvB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	390 — L1 transposable element, trimerization domain

Domain ID domain_id	3brvC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2110 —

Domain ID domain_id	3brvD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	390 — L1 transposable element, trimerization domain

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Unit-cell length a length_a	44.820 Å
Unit-cell length b length_b	50.670 Å
Unit-cell length c length_c	102.790 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	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	45.450 Å
R factor r_factor	0.2122
R_work r_work	0.2082
R_free r_free	0.2940

NEMO/IKKb association domain structure

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

Inhibitor of nuclear factor kappa-B kinase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

NF-kappa-B essential modulator

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

3brv__assembly_3__model_1

3brv__assembly_3__model_1 | I(q)

3brv__assembly_3__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

NEMO/IKKb association domain structure

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

Inhibitor of nuclear factor kappa-B kinase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NF-kappa-B essential modulator

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

3brv__assembly_3__model_1

3brv__assembly_3__model_1 | I(q)

3brv__assembly_3__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)