2K8B: Ubiquitin

Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin. Determined by solution NMR. Released 5 May 2009.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 1,240
Mol. weight: 17.61 kDa
Released: 5 May 2009

Explore 2K8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2K8B contains 5 α-helices and 11 β-strands across 2 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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-33	11
β-strand	41-45	5	1
β-strand	48-49	2	1
β-strand	55	1	2
α-helix	61-62	2
β-strand	66-71	6	1

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	57-59	3	3
β-strand	62-64	3	3
β-strand	66-70	5	4
α-helix	78	1
β-strand	79-83	5	4
α-helix	89-100	12
α-helix	105-119	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Phospholipase A-2-activating protein	B	protein	80	Homo sapiens	Q9Y263 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2K8B_1 Ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>2K8B_2 Phospholipase A-2-activating protein (chains B)
ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLD
QVAKFIIDNTKGQMLGLGNP

Primary citation

Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein. Fu, Q.S., Zhou, C.J., Gao, H.C. et al. J Biol Chem (2009) 284:19043-19052. DOI 10.1074/jbc.M109.009126 · 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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