5XIT: RNF168 UDM1

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II. Determined by X-ray diffraction at 2.25 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 3,740
Mol. weight: 54.71 kDa
Ligands: PR
Released: 7 Mar 2018

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

Secondary structure: helices and β-sheets

5XIT contains 15 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	114-186	73

Chains B and D: 3 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	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
β-strand	66-71	6	5

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	117-185	69

Chain F: 3 helices, 7 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	55	1	8
β-strand	66-71	6	7

Chain H: 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
β-strand	66-71	6	3
α-helix	72-73	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-40S ribosomal protein S27a	D, F	protein	76	Mus musculus	P62983 (AlphaFold model)
E3 ubiquitin-protein ligase RNF168	A, E	protein	81	Homo sapiens	Q8IYW5 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	B, H	protein	77	Mus musculus	P62983 (AlphaFold model)

Sequence of entity 1 (D, F), FASTA

>5XIT_1 Ubiquitin-40S ribosomal protein S27a (chains D, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQRESTLHLVLRLRGG

Sequence of entity 2 (A, E), FASTA

>5XIT_2 E3 ubiquitin-protein ligase RNF168 (chains A, E)
GPGHMPGELRREYEEEISKVAAERRASEEEENKASEEYIQRLLAEEEEEEKRQAEKRRRA
MEEQLKSDEELARKLSIDINN

Sequence of entity 3 (B, H), FASTA

>5XIT_3 Ubiquitin-40S ribosomal protein S27a (chains B, H)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGD

Ligands and cofactors

ID	Name	Formula	Copies
PR	Praseodymium ion	Pr	3

Water and common crystallization additives (GOL) are not listed.

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 P62983 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XIS 1.78 Å, Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I
5XIU 1.8 Å, Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin
7E62 1.99 Å, Mouse TAB2 NZF in complex with Lys6-linked diubiquitin
3VHT 2.4 Å, Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin
31FX 2.54 Å, Mouse 80S ribosome, sgRNA control
31FY 2.57 Å, Mouse 80S ribosome, Gm10076 KO
9QOH 2.78 Å, Mouse Ribosome POST translocation state
31FZ 2.89 Å, Mouse 80S ribosome, eL41 KO
9QQL 3.09 Å, Mouse RPS15 P131 Mutant Ribosome POST translocation state
7LS2 3.1 Å, 80S ribosome from mouse bound to eEF2 (Class I)
7LS1 3.3 Å, 80S ribosome from mouse bound to eEF2 (Class II)
9QZP 3.43 Å, Mouse Ribosome Classical Pre translocation state

Browse structure collections

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