7EB9: A20-binding inhibitor of NF-kB 1

The structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin. Determined by X-ray diffraction at 3.2 Å resolution. Released 21 Jul 2021.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,333
Mol. weight: 57.05 kDa
Released: 21 Jul 2021

Explore 7EB9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EB9 contains 13 α-helices and 28 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	13-16	4	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	1
β-strand	49	1	1
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1
β-strand	102-106	5	3
β-strand	112-116	5	3
β-strand	122	1	4
α-helix	123-134	12
α-helix	138-140	3
β-strand	141-145	5	3
β-strand	148-149	2	3
β-strand	155	1	4
β-strand	166-171	6	3
β-strand	201-207	7	5
β-strand	212-217	6	5
β-strand	222	1	6
α-helix	223-234	12
α-helix	238-240	3
β-strand	241-245	5	5
β-strand	248-249	2	5
α-helix	250-251	2
β-strand	255	1	6
β-strand	266-271	6	5
β-strand	301-306	6	7
β-strand	312-317	6	7
β-strand	322	1	8
α-helix	323-334	12
α-helix	338-340	3
β-strand	343-344	2	7
β-strand	349	1	7
β-strand	355	1	8
α-helix	357-359	3
β-strand	366-369	4	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	453-502	50

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	448-502	55

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
tetra ubiquitin	A	protein	304	Homo sapiens	P0CG48 (AlphaFold model)
TNFAIP3-interacting protein 1	B, C	protein	99	Homo sapiens	Q15025 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7EB9_1 tetra ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA
KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT
ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
LRGG

Sequence of entity 2 (B, C), FASTA

>7EB9_2 TNFAIP3-interacting protein 1 (chains B, C)
EIQRLNKALEEALSIQTPPSSPPTAFGSPEGAGALLRKQELVTQNELLKQQVKIFEEDFQ
RERSDRERMNEEKEELKKQVEKLQAQVTLSNTQLKAFKD

Primary citation

Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-kappa B 1 (ABIN1) and M1-Linked Ubiquitins. Hong, J.Y., Lin, S.C., Kuo, B.J. et al. J Mol Biol (2021) 433:167116-167116. DOI 10.1016/j.jmb.2021.167116 · PubMed

Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
4HK2 1.4 Å, U7Ub25.2540
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant

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