2QHO: UBA domain from EDD ubiquitin ligase

Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin. Determined by X-ray diffraction at 1.85 Å resolution. Released 25 Sept 2007.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Bos taurus, Homo sapiens
Chains: 8
Atoms: 4,144
Mol. weight: 57.59 kDa
Released: 25 Sept 2007

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

Secondary structure: helices and β-sheets

2QHO contains 35 α-helices and 28 β-strands across 8 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	2-7	6	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	56-59	4
β-strand	66-71	6	1

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	182-184	3
α-helix	187-196	10
α-helix	202-211	10
α-helix	216-224	9

Chains C and E: 5 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
α-helix	57-59	3
β-strand	66-71	6	3
α-helix	72-74	3

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	179-181	3
α-helix	182-184	3
α-helix	187-196	10
α-helix	202-211	10
α-helix	216-225	10

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	182-184	3
α-helix	187-196	10
α-helix	202-211	10
α-helix	216-227	12

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7

Chain H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	182-184	3
α-helix	187-196	10
α-helix	202-211	10
α-helix	216-225	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, C, E, G	protein	76	Bos taurus	P0CH28 (AlphaFold model)
E3 ubiquitin-protein ligase EDD1	B, D, F, H	protein	53	Homo sapiens	O95071

Sequence of entity 1 (A, C, E, G), FASTA

>2QHO_1 Ubiquitin (chains A, C, E, G)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B, D, F, H), FASTA

>2QHO_2 E3 ubiquitin-protein ligase EDD1 (chains B, D, F, H)
GSIPASVIPEELISQAQVVLQGKSRSVIIRELQRTNLDVNLAVNNLLSRDDED

Primary citation

Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD. Kozlov, G., Nguyen, L., Lin, T. et al. J Biol Chem (2007) 282:35787-35795. DOI 10.1074/jbc.M705655200 · PubMed

Other PDB entries of the same protein (UniProt P0CH28 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WWZ 1.4 Å, TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121
2ZCC 1.4 Å, Ubiquitin crystallized under high pressure
3M3J 1.6 Å, A new crystal form of Lys48-linked diubiquitin
4XYZ 1.65 Å, Crystal structure of K33 linked di-Ubiquitin
1P3Q 1.7 Å, Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9
2D3G 1.7 Å, Double sided ubiquitin binding of Hrs-UIM
6A42 1.7 Å, R1EN(5-223)-ubiquitin fusion
1WRD 1.75 Å, Crystal structure of Tom1 GAT domain in complex with ubiquitin
1UZX 1.85 Å, A complex of the Vps23 UEV with ubiquitin
2HD5 1.85 Å, USP2 in complex with ubiquitin
2OOB 1.9 Å, crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin
2C7N 2.1 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin

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