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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 701–745 Chain C； UniProt 701–745	Fragment：NEMO-binding	NF-kappa-B essential modulator × 2 （Q9Y6K9）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 701–745	Fragment：NEMO-binding	NF-kappa-B essential modulator × 1 （Q9Y6K9）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 701–745	Fragment：NEMO-binding	NF-kappa-B essential modulator × 1 （Q9Y6K9）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 701–745	Fragment：NEMO-binding	NF-kappa-B essential modulator × 1 （Q9Y6K9）	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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 701–745	Fragment：NEMO-binding	NF-kappa-B essential modulator × 1 （Q9Y6K9）	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

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 3BRV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BRT NEMO/IKK association domain structure Deposited 2007-12-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A Chain C 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A	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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A	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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A	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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A	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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A	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
4E3C X-ray crystal structure of human IKK2 in an active conformation Deposited 2012-03-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 11–669（659 aa） Fragment：UNP Residues 11-669 Chain F 11–669（659 aa） Fragment：UNP Residues 11-669	Mutation：S177E, S181E Mutation：S177E, S181E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.98 Å R-free 0.299
4E3C X-ray crystal structure of human IKK2 in an active conformation Deposited 2012-03-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 11–669（659 aa） Fragment：UNP Residues 11-669 Chain C 11–669（659 aa） Fragment：UNP Residues 11-669	Mutation：S177E, S181E Mutation：S177E, S181E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.98 Å R-free 0.299
4E3C X-ray crystal structure of human IKK2 in an active conformation Deposited 2012-03-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 11–669（659 aa） Fragment：UNP Residues 11-669 Chain E 11–669（659 aa） Fragment：UNP Residues 11-669	Mutation：S177E, S181E Mutation：S177E, S181E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.98 Å R-free 0.299
4KIK Human IkB kinase beta Deposited 2013-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–664（663 aa） Chain B 2–664（663 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	KSA K-252A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.83 Å R-free 0.236
8OMV Crystal structure of the constitutively active S117E/S181E mutant of human IKK2 Deposited 2023-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–669（669 aa） Chain B 1–669（669 aa）	Mutation：S177E, S181E Mutation：S177E, S181E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol	Resolution 4.16 Å R-free 0.299
8OMV Crystal structure of the constitutively active S117E/S181E mutant of human IKK2 Deposited 2023-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–669（669 aa） Chain D 1–669（669 aa）	Mutation：S177E, S181E Mutation：S177E, S181E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol	Resolution 4.16 Å R-free 0.299
8OMV Crystal structure of the constitutively active S117E/S181E mutant of human IKK2 Deposited 2023-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–669（669 aa）	Mutation：S177E, S181E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol	Resolution 4.16 Å R-free 0.299

4 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 44–111 Chain D； UniProt 44–111	Fragment：UNP residues 44-111	Inhibitor of nuclear factor kappa-B kinase subunit beta × 2 （O14920）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 44–111	Fragment：UNP residues 44-111	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 44–111	Fragment：UNP residues 44-111	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 44–111	Fragment：UNP residues 44-111	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920）	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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 44–111	Fragment：UNP residues 44-111	Inhibitor of nuclear factor kappa-B kinase subunit beta × 1 （O14920）	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

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 3BRV	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 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 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 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 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 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 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
3CL3 Crystal Structure of a vFLIP-IKKgamma complex: Insights into viral activation of the IKK signalosome Deposited 2008-03-18	Different construct 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 oligomeric state 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 oligomeric state 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 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
6MI3 Structure of NEMO(51-112) with N- and C-terminal coiled-coil adaptors. Deposited 2018-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 119–180（62 aa） Chain B 119–180（62 aa）	Mutation：E56A, E57A, C76A, C95S Mutation：E56A, E57A, C76A, C95S	No recorded non-water small molecule	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
7T2U SARS-CoV2 3C-Like protease complexed with Nemo peptide Deposited 2021-12-06	Different construct 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 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 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 16 assemblies. Open the comparison page and filter oligomeric states

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

Radius of gyration Rg (Guinier) rg_guinier	24.29 Å
Radius of gyration Rg (electron density) rg_electron	24.83 Å
Forward intensity I(0) i0	10300000.00
Molecular weight molecular_weight	23028.0 kDa
Excluded volume excluded_volume	28402 Å³
Envelope volume envelope_volume	35606 Å³
Hydration-shell volume shell_volume	14548 Å³
Envelope diameter envelope_diameter	96.5 Å
Shell Rg shell_rg	26.99 Å
Envelope Rg envelope_rg	25.54 Å
Shape Rg shape_rg	24.81 Å
Total Rg total_rg	25.19 Å
Total atoms total_atoms	1616
Residues n_residues	204
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	94.4 Å
Rg (real space) rg_real	24.93 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	1.0300e+07
I(0) uncertainty (real space) i0_real_error	1.5610e+05
Rg (reciprocal space) rg_reciprocal	24.78 Å
I(0) (reciprocal space) i0_reciprocal	10300000.0000
Solution quality estimate total_estimate	0.6603
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.772
Kurtosis Kurtosis kurtosis	-0.005
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7139000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.186; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.026; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/br/3brv/3brv.fit
pddf	/app/data/pr_computation/br/3brv/3brv.pr.out
profile	/app/data/saxs_computation/br/3brv/3brv.dat

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

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)