2LVP: Gp78CUE domain

gp78CUE domain bound to the distal ubiquitin of K48-linked diubiquitin. Determined by solution NMR. Released 21 Nov 2012.

Method: Solution NMR
Organism: Homo sapiens
Chains: 3
Atoms: 1,623
Mol. weight: 23.12 kDa
Released: 21 Nov 2012

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

Secondary structure: helices and β-sheets

2LVP contains 11 α-helices and 14 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: 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	23-33	11
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	23-33	11
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	56-58	3
β-strand	66-71	6	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	455-467	13
α-helix	473-479	7
α-helix	486-495	10
α-helix	499-500	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
E3 ubiquitin-protein ligase AMFR	C	protein	52	Homo sapiens	Q9UKV5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2LVP_1 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (C), FASTA

>2LVP_2 E3 ubiquitin-protein ligase AMFR (chains C)
SNSQLNAMAHQIQEMFPQVPYHLVLQDLQLTRSVEITTDNILEGRIQVPFPT

Primary citation

Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains. Liu, S., Chen, Y., Li, J. et al. Structure (2012) 20:2138-2150. DOI 10.1016/j.str.2012.09.020 · 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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