SAXSdb — 9azj

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

NF-kappa-B essential modulator

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	E3 ubiquitin-protein ligase RNF31 × 2 （Q96EP0） Ubiquitin × 3 （P0CG47） ZINC ION × 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 257–364 Author chain B； PDBConstruct 1–108； UniProt 257–364 Author chain C； PDBConstruct 1–108； UniProt 257–364 Author chain D； PDBConstruct 1–108； UniProt 257–364

E3 ubiquitin-protein ligase RNF31

Homo sapiens

UniProt Q96EP0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	NF-kappa-B essential modulator × 4 （Q9Y6K9） Ubiquitin × 3 （P0CG47） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNF31_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–29； UniProt 351–379 Author chain G； PDBConstruct 1–29； UniProt 351–379

Ubiquitin

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	NF-kappa-B essential modulator × 4 （Q9Y6K9） E3 ubiquitin-protein ligase RNF31 × 2 （Q96EP0） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain S； PDBConstruct 1–76； UniProt 1–76 Author chain Z； PDBConstruct 1–76； UniProt 1–76

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	9azj
Deposition date deposition_date	2024-03-11
Structure title title	Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1
Keywords keywords	ubiquitin binding domain, UBAN, NZF, NF-kB, SIGNALING PROTEIN, NEMO; SIGNALING 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.

9azj__assembly_1__model_1

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

Download this curve (.dat)

9azj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9azj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.36 Å
Rg (electron density)	34.83 Å
Total Rg	34.79 Å
Atom count	4258
Residues	589
Excluded volume	75550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9azj__assembly_1__model_1`	nonameric （9）	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	NF-kappa-B essential modulator
Molecular weight formula_weight	12643.4 kDa
Mutation mutation	K285C
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	4258

GMQLEDLKQQLQQAEEALVAKQEVIDKLCEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREYSKLKASCQESARIEDMRKRHVEVS

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

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase RNF31
Molecular weight formula_weight	3245.7 kDa
EC 编号 ec_number	2.3.2.31
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G

RGRWACQSCTFENEAAAVLCSICERPRLA

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

Entity 3 Entity 3 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8622.9 kDa
Mutation mutation	G76C
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,S,Z

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC

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

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	66.828 Å
Unit-cell length b length_b	101.447 Å
Unit-cell length c length_c	144.140 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.320 Å
Low-resolution limit resolution_low	50.720 Å
R factor r_factor	0.2431
R_work r_work	0.2408
R_free r_free	0.2847

Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1

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

NF-kappa-B essential modulator

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase RNF31

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

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

9azj__assembly_1__model_1

9azj__assembly_1__model_1 | I(q)

9azj__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

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)

Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1

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

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

E3 ubiquitin-protein ligase RNF31

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin

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

9azj__assembly_1__model_1

9azj__assembly_1__model_1 | I(q)

9azj__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

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)