6IF1: Ube2K and K48-linked di-ubiquitin complex

Crystal structure of Ube2K and K48-linked di-ubiquitin complex. Determined by X-ray diffraction at 2.47 Å resolution. Released 21 Nov 2018.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,366
Mol. weight: 61.79 kDa
Released: 21 Nov 2018

Explore 6IF1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IF1 contains 29 α-helices and 30 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: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	20-23	4
β-strand	27-31	5	1
β-strand	38-44	7	1
α-helix	45-46	2
β-strand	55-61	7	1
α-helix	70-71	2
β-strand	72-75	4	1
β-strand	84	1	2
β-strand	90	1	1
β-strand	91	1	2
α-helix	94-96	3
α-helix	106-118	13
α-helix	128-136	9
α-helix	138-153	16
α-helix	160-170	11
α-helix	176-185	10
α-helix	190-198	9

Chain B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	20-23	4
β-strand	27-31	5	3
β-strand	38-44	7	3
α-helix	45-46	2
β-strand	55-61	7	3
α-helix	70-71	2
β-strand	72-75	4	3
β-strand	84	1	4
β-strand	90	1	3
β-strand	91	1	4
α-helix	94-96	3
α-helix	106-118	13
α-helix	128-136	9
α-helix	138-153	16
α-helix	160-171	12
α-helix	176-185	10
α-helix	190-198	9

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
β-strand	66-69	4	5
α-helix	71-73	3

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	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	52	1	9
β-strand	54	1	9
β-strand	55	1	8
β-strand	66-71	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 K	A, B	protein	199	Homo sapiens	P61086 (AlphaFold model)
Ubiquitin	C, D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6IF1_1 Ubiquitin-conjugating enzyme E2 K (chains A, B)
MANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQLEI
KIPETYPFNPPKVRFITKIWHPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALLAAA
EPDDPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLCAMGFDRNAVI
VALSSKSWDVETATELLLS

Sequence of entity 2 (C, D), FASTA

>6IF1_2 Ubiquitin (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis. Lee, J.G., Youn, H.S., Kang, J.Y. et al. Biochem Biophys Res Commun (2018) 506:102-107. DOI 10.1016/j.bbrc.2018.10.067 · PubMed

Other PDB entries of the same protein (UniProt P61086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3K9O 1.8 Å, The crystal structure of E2-25K and UBB+1 complex
3E46 1.86 Å, Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington interacting…
5DFL 2.1 Å, Crystal structure of Ube2K~Ubiquitin conjugate
6JB7 2.1 Å, Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A…
3F92 2.23 Å, Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington Interacting…
7MYH 2.39 Å, Ubiquitin variant UbV.k.2 in complex with Ube2k
1YLA 2.4 Å, Ubiquitin-conjugating enzyme E2-25 kDa (Huntington interacting protein 2)
7OJX 2.4 Å, E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for…
2O25 2.6 Å, Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9
6JB6 2.7 Å, Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A…
3K9P 2.8 Å, The crystal structure of E2-25K and ubiquitin complex
7MYF 3.0 Å, Ubiquitin variant UbV.k.1 in complex with Ube2k

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