3M3J: A new crystal form of Lys48-linked diubiquitin

A new crystal form of Lys48-linked diubiquitin. Determined by X-ray diffraction at 1.6 Å resolution. Released 23 Mar 2010.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Bos taurus
Chains: 6
Atoms: 4,341
Mol. weight: 51.81 kDa
Released: 23 Mar 2010

Explore 3M3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M3J contains 23 α-helices and 42 β-strands across 6 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.

Chains A, C, D, E and F: 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	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	1
β-strand	12-16	5	1
β-strand	22	1	3
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
β-strand	55	1	3
α-helix	57-59	3
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B, C, D, E, F	protein	76	Bos taurus	P0CH28 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3M3J_1 Ubiquitin (chains A, B, C, D, E, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

A new crystal form of Lys48-linked diubiquitin. Trempe, J.F., Brown, N.R., Noble, M.E. et al. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 66:994-998. DOI 10.1107/S1744309110027600 · 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
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
2QHO 1.85 Å, Crystal structure of the UBA domain from EDD ubiquitin ligase 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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