3JSV: Mouse NEMO CoZi

Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Oct 2009.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 2,652
Mol. weight: 39.51 kDa
Released: 27 Oct 2009

Explore 3JSV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JSV contains 12 α-helices and 14 β-strands across 4 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
β-strand	66-71	6	3

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	253-317	65
α-helix	321-331	11

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	257-288	32
α-helix	291-335	45
α-helix	337-340	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin	B	protein	77	Homo sapiens	P0CG48 (AlphaFold model)
NF-kappa-B essential modulator	C, D	protein	94	Mus musculus	O88522 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3JSV_1 Ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQRESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>3JSV_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGD

Sequence of entity 3 (C, D), FASTA

>3JSV_3 NF-kappa-B essential modulator (chains C, D)
GMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAER
HAREKLVEKKEYLQEQLEQLQREFNKLKVGCHES

Primary citation

Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin. Yoshikawa, A., Sato, Y., Yamashita, M. et al. FEBS Lett (2009) 583:3317-3322. DOI 10.1016/j.febslet.2009.09.028 · 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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