SAXSdb — 2v4h

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

NF-KAPPA-B ESSENTIAL MODULATOR

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	1D5 DARPIN × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEMO_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–110； UniProt 251–337 Author chain B； PDBConstruct 24–110； UniProt 251–337

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	2v4h
Deposition date deposition_date	2008-09-22
Structure title title	NEMO CC2-LZ domain - 1D5 DARPin complex
Keywords keywords	TRANSCRIPTION, METAL-BINDING, NEMO - IKK GAMMA - NFKB PATHWAY -DARPIN, TRANSCRIPTION REGULATION; 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.

2v4h__assembly_1__model_1

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

Download this curve (.dat)

2v4h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v4h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.44 Å
Rg (electron density)	55.43 Å
Total Rg	55.06 Å
Atom count	6982
Residues	884
Excluded volume	123230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v4h__assembly_1__model_1`	octameric （8）	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	NF-KAPPA-B ESSENTIAL MODULATOR
Molecular weight formula_weight	12895.6 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	3542

MGSSHHHHHHSSGLVPRGSHMASMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERHAREKLVEKKEYLQEQLEQLQREFNKLK

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

Entity 2 Entity 2 polymer

Description description	1D5 DARPIN
Molecular weight formula_weight	14924.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

HHHHHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNANDRKGNTPLHLAADYDHLEIVEVLLKHGADVNAHDNDGSTPLHLAALFGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Source Source

Source organism organism	SYNTHETIC CONSTRUCT
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2v4hA00
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	990 — Nemo cc2-lz domain - 1d5 darpin complex

Domain ID domain_id	2v4hB00
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	990 — Nemo cc2-lz domain - 1d5 darpin complex

Domain ID domain_id	2v4hC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	2v4hD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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Unit-cell length a length_a	63.020 Å
Unit-cell length b length_b	63.020 Å
Unit-cell length c length_c	436.917 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	47.670 Å
R factor r_factor	0.2105
R_work r_work	0.2075
R_free r_free	0.2682

NEMO CC2-LZ domain - 1D5 DARPin complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2v4h__assembly_1__model_1

2v4h__assembly_1__model_1 | I(q)

2v4h__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

NEMO CC2-LZ domain - 1D5 DARPin complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2v4h__assembly_1__model_1

2v4h__assembly_1__model_1 | I(q)

2v4h__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)