SAXSdb — 6mi3

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

NF-kB ESSENTIAL MODULATOR,NF-kappa-B essential modulator,NF-kB ESSENTIAL MODULATOR

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 119–180 Chain B； UniProt 119–180	Mutation：E56A, E57A, C76A, C95S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1 M Tris pH 8.0, 5.8% PGA-LM, 5.45% PEG 20,000	Resolution 1.78 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6MI3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JVX Solution Structure of human NEMO zinc finger Deposited 2007-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–419（26 aa） Fragment：zinc finger domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1 mM NEMO ZF, 2 mM ZnS04, 2 mM TCEP, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JVY Solution Structure of the EDA-ID-related C417F mutant of human NEMO zinc finger Deposited 2007-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–419（26 aa） Fragment：zinc finger domain	Mutation：C417F	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1 mM NEMO ZF-C417F, 2 mM ZnS04, 2 mM TCEP, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3BRT NEMO/IKK association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 44–111（68 aa） Chain D 44–111（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K	Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–111（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K	Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 44–111（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K	Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 44–111（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K	Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–111（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K	Resolution 2.25 Å R-free 0.282
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 44–111（68 aa） Fragment：UNP residues 44-111 Chain D 44–111（68 aa） Fragment：UNP residues 44-111	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–111（68 aa） Fragment：UNP residues 44-111	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 44–111（68 aa） Fragment：UNP residues 44-111	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 44–111（68 aa） Fragment：UNP residues 44-111	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–111（68 aa） Fragment：UNP residues 44-111	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.294
3CL3 Crystal Structure of a vFLIP-IKKgamma complex: Insights into viral activation of the IKK signalosome Deposited 2008-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 150–272（123 aa） Fragment：residues 150-272 Chain E 150–272（123 aa） Fragment：residues 150-272	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；225mM Tris pH 7.5, 4% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.20 Å R-free 0.287
3FX0 Crystal structure of Human NEMO CC2_LZ domain Deposited 2009-01-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 246–337（92 aa） Fragment：CC2_LZ domain Chain B 246–337（92 aa） Fragment：CC2_LZ domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；10% PEG 1000, 10% PEG 4000, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.20 Å R-free 0.306
4BWN NEMO CC2-LZ DOMAIN Deposited 2013-07-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 258–344（87 aa） Fragment：CC2-LZ DOMAIN, RESIDUES 258-344 Chain B 258–344（87 aa） Fragment：CC2-LZ DOMAIN, RESIDUES 258-344	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM LITHIUM CHLORIDE, 10MM HEPES PH 7,5 AND 25% PEG 6000	Resolution 2.27 Å R-free 0.246
5AAY TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy Deposited 2015-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 392–419（28 aa） Fragment：RESIDUES 392-419	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0 NMR sample composition 95% WATER/5% D2O	Resolution not provided
7T2U SARS-CoV2 3C-Like protease complexed with Nemo peptide Deposited 2021-12-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 226–235（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG3350, 0.1M Bis-Tris (pH 6.5)	Resolution 2.10 Å R-free 0.300
7T2U SARS-CoV2 3C-Like protease complexed with Nemo peptide Deposited 2021-12-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 226–235（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG3350, 0.1M Bis-Tris (pH 6.5)	Resolution 2.10 Å R-free 0.300
7TV4 Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin Deposited 2022-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 257–346（90 aa） Chain D 257–346（90 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5, 22% v/v PEG Smear Broad	Resolution 4.20 Å R-free 0.286
9AZJ Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Deposited 2024-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 257–364（108 aa） Chain B 257–364（108 aa） Chain C 257–364（108 aa） Chain D 257–364（108 aa）	Mutation：K285C Mutation：K285C Mutation：K285C Mutation：K285C	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.6；293 K；150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol	Resolution 3.32 Å R-free 0.285

11 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEMO_HUMAN
Isoform	Q9Y6K9-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 33–94； UniProt 119–180 Author chain B； PDBConstruct 33–94； UniProt 119–180

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	6mi3
Deposition date deposition_date	2018-09-19
Structure title title	Structure of NEMO(51-112) with N- and C-terminal coiled-coil adaptors.
Keywords keywords	coiled coil, scaffolding, NF-kB pathway, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	48.34 Å
Radius of gyration Rg (electron density) rg_electron	52.32 Å
Forward intensity I(0) i0	13754400.00
Molecular weight molecular_weight	28977.0 kDa
Excluded volume excluded_volume	36296 Å³
Envelope volume envelope_volume	57251 Å³
Hydration-shell volume shell_volume	13447 Å³
Envelope diameter envelope_diameter	183.5 Å
Shell Rg shell_rg	33.40 Å
Envelope Rg envelope_rg	53.88 Å
Shape Rg shape_rg	52.33 Å
Total Rg total_rg	51.00 Å
Total atoms total_atoms	2037
Residues n_residues	246
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	185.6 Å
Rg (real space) rg_real	50.41 Å
Rg uncertainty (real space) rg_real_error	3.36 Å
I(0) (real space) i0_real	1.3750e+07
I(0) uncertainty (real space) i0_real_error	2.8860e+05
Rg (reciprocal space) rg_reciprocal	48.35 Å
I(0) (reciprocal space) i0_reciprocal	13720000.0000
Solution quality estimate total_estimate	0.5534
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.9 Å
Skewness Skewness skewness	0.695
Kurtosis Kurtosis kurtosis	-0.322
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	651700.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.007; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.013; Smooth: 0.158

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	64.480 Å
Unit-cell length b length_b	33.620 Å
Unit-cell length c length_c	76.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.783 Å
Low-resolution limit resolution_low	37.754 Å
R factor r_factor	0.2441
R_work r_work	0.2428
R_free r_free	0.2661

Description description	NF-kB ESSENTIAL MODULATOR,NF-kappa-B essential modulator,NF-kB ESSENTIAL MODULATOR
Molecular weight formula_weight	14641.8 kDa
Mutation mutation	E56A, E57A, C76A, C95S
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2227

Structure of NEMO(51-112) with N- and C-terminal coiled-coil adaptors.

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

NF-kB ESSENTIAL MODULATOR,NF-kappa-B essential modulator,NF-kB ESSENTIAL MODULATOR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	183

fit	/app/data/saxs_computation/mi/6mi3/6mi3.fit
pddf	/app/data/pr_computation/mi/6mi3/6mi3.pr.out
profile	/app/data/saxs_computation/mi/6mi3/6mi3.dat