6GF1: Ubiquitin D

The structure of the ubiquitin-like modifier FAT10 reveals a novel targeting mechanism for degradation by the 26S proteasome. Determined by X-ray diffraction at 1.93 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,942
Mol. weight: 28.88 kDa
Released: 29 Aug 2018

Explore 6GF1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GF1 contains 16 α-helices and 21 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
α-helix	15-16	2
β-strand	17-21	5	1
β-strand	26	1	2
α-helix	27-38	12
α-helix	42-44	3
β-strand	45-49	5	1
β-strand	52-53	2	1
α-helix	54-55	2
β-strand	59	1	2
α-helix	61-63	3
β-strand	70-77	8	1

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	3
α-helix	16	1
β-strand	17-21	5	3
β-strand	26	1	4
α-helix	27-38	12
α-helix	42-44	3
β-strand	45-49	5	3
β-strand	52-53	2	3
α-helix	54-55	2
β-strand	59	1	4
α-helix	61-63	3
α-helix	65-67	3
β-strand	70-77	8	3

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	5
α-helix	15-16	2
β-strand	17-21	5	5
β-strand	26	1	6
α-helix	27-38	12
α-helix	42-44	3
β-strand	45-49	5	5
β-strand	52-53	2	5
α-helix	54-55	2
β-strand	59	1	6
α-helix	60	1
β-strand	70-77	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin D	A, B, C	protein	83	Homo sapiens	O15205 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6GF1_1 Ubiquitin D (chains A, B, C)
GASTLTVHVRSEEWDLMTFDANPYDSVKKIKEHVRSKTKVPVQDQVLLLGSKILKPRRSL
SSYGIDKEKTIHLTLKVVKPSDE

Primary citation

The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation. Aichem, A., Anders, S., Catone, N. et al. Nat Commun (2018) 9:3321-3321. DOI 10.1038/s41467-018-05776-3 · PubMed

Other PDB entries of the same protein (UniProt O15205 (AlphaFold model), which also has an AlphaFold model), best resolution first:

28MJ 2.77 Å, Cryo-EM structure of UBA6 in complex with FAT10 in the pre-adenylation state.
28MQ 3.04 Å, Cryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex
9E8O 3.1 Å, Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt2 at top of spiral…
7PYV 3.27 Å, Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10
28MK 3.53 Å, Cryo-EM structure of UBA6 in complex with FAT10 in the post-thiolation state.
2MBE Backbone 1H and 15N Chemical Shift Assignments for the first domain of FAT10
6GF2 The structure of the ubiquitin-like modifier FAT10 reveals a novel targeting mechanism…

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