5XIS: RNF168 UDM1

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I. Determined by X-ray diffraction at 1.78 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 4,048
Mol. weight: 54.84 kDa
Ligands: XYZ, MG
Released: 7 Mar 2018

Explore 5XIS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XIS contains 17 α-helices and 28 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.

Chain A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	115-187	73

Chain B: 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	23-34	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

Chains C and F: 4 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

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	110-112	3
α-helix	115-187	73

Chain E: 2 helices, 7 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF168	A, D	protein	84	Homo sapiens	Q8IYW5 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	B, E	protein	77	Mus musculus	P62983 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	C, F	protein	76	Mus musculus	P62983 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5XIS_1 E3 ubiquitin-protein ligase RNF168 (chains A, D)
GPGHMLSKPGELRREYEEEISKVAAERRASEEEENKASEEYIQRLLAEEEEEEKRQAEKR
RRAMEEQLKSDEELARKLSIDINN

Sequence of entity 2 (B, E), FASTA

>5XIS_2 Ubiquitin-40S ribosomal protein S27a (chains B, E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGD

Sequence of entity 3 (C, F), FASTA

>5XIS_3 Ubiquitin-40S ribosomal protein S27a (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQRESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
XYZ	beta-D-xylofuranose	C5 H10 O5	2
MG	Magnesium ion	Mg	2

Primary citation

Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Takahashi, T.S., Hirade, Y., Toma, A. et al. Nat Commun (2018) 9:170-170. DOI 10.1038/s41467-017-02345-y · PubMed

Other PDB entries of the same protein (UniProt Q8IYW5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XIU 1.8 Å, Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
3L11 2.12 Å, Crystal Structure of the Ring Domain of RNF168
5XIT 2.25 Å, Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II
8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
5YDK 2.5 Å, Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form
4GB0 2.6 Å, Crystal Structure of the RING domain of RNF168
8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
8SMX 3.2 Å, Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and…
8SMY 3.2 Å, Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and…

Browse structure collections

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