3L11: Ring Domain of RNF168

Crystal Structure of the Ring Domain of RNF168. Determined by X-ray diffraction at 2.12 Å resolution. Released 19 Jan 2010.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Homo sapiens
Chains: 1
Atoms: 891
Mol. weight: 13.47 kDa
Ligands: ZN, MLI
Released: 19 Jan 2010

Explore 3L11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L11 contains 8 α-helices and 7 β-strands across 1 chain. 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	7-10	4
α-helix	11-14	4
β-strand	15	1	1
β-strand	22	1	1
β-strand	27-28	2	2
β-strand	34-35	2	2
α-helix	37-40	4
α-helix	41-45	5
β-strand	50	1	3
β-strand	57	1	3
α-helix	59-67	9
β-strand	72	1	2
α-helix	74-83	10
α-helix	85-93	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF168	A	protein	115	Homo sapiens	Q8IYW5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3L11_1 E3 ubiquitin-protein ligase RNF168 (chains A)
GSMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV
SSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGQESEEVADDYQPVRLLSKP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MLI	Malonate ion	C3 H2 O4	2

Primary citation

Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation. Campbell, S.J., Edwards, R.A., Leung, C.C. et al. J Biol Chem (2012) 287:23900-23910. DOI 10.1074/jbc.M112.359653 · PubMed

Other PDB entries of the same protein (UniProt Q8IYW5 (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
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
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…

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