SAXSdb — 7tv4

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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 5	Polyubiquitin-C × 2 （P0CG48） E3 ubiquitin-protein ligase RNF31 × 1 （Q96EP0） ZINC ION × 1 water × 4	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 B； PDBConstruct 9–98； UniProt 257–346 Author chain D； PDBConstruct 9–98； UniProt 257–346

Polyubiquitin-C

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	NF-kappa-B essential modulator × 2 （Q9Y6K9） E3 ubiquitin-protein ligase RNF31 × 1 （Q96EP0） ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–156； UniProt 77–228 Author chain G； PDBConstruct 5–156； UniProt 77–228

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 5	NF-kappa-B essential modulator × 2 （Q9Y6K9） Polyubiquitin-C × 2 （P0CG48） ZINC ION × 1 water × 4	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	3
Chains and sequence ranges	Author chain K； PDBConstruct 6–35； UniProt 350–379

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	7tv4
Deposition date deposition_date	2022-02-03
Structure title title	Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin
Keywords keywords	SIGNALING PROTEIN, Ubiquitin signaling, NF-kappa B signaling; 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.

7tv4__assembly_1__model_1

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

Download this curve (.dat)

7tv4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7tv4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.91 Å
Rg (electron density)	32.87 Å
Total Rg	33.17 Å
Atom count	3895
Residues	486
Excluded volume	69792 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7tv4__assembly_1__model_1`	pentameric （5）	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	NF-kappa-B essential modulator
Molecular weight formula_weight	11293.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	3906

GPLGSPEFGMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREYSKLKAS

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	Polyubiquitin-C
Molecular weight formula_weight	17423.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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	E3 ubiquitin-protein ligase RNF31
Molecular weight formula_weight	3728.3 kDa
EC 编号 ec_number	2.3.2.31
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GPLGSARGRWACQSCTFENEAAAVLCSICERPRLA

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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Unit-cell length a length_a	55.950 Å
Unit-cell length b length_b	69.560 Å
Unit-cell length c length_c	180.050 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	56.010 Å
R factor r_factor	0.2254
R_work r_work	0.2221
R_free r_free	0.2858

Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin

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

Polyubiquitin-C

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7tv4__assembly_1__model_1

7tv4__assembly_1__model_1 | I(q)

7tv4__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 (5)

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

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin

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

Polyubiquitin-C

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7tv4__assembly_1__model_1

7tv4__assembly_1__model_1 | I(q)

7tv4__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 (5)

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

Entity 5 Entity 5 water

7. Citations (1)