7M4O: Phosphorylated RBR E3 ligase RNF216

Name: PDB 7M4O: Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin
Published: 2022-01-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin. Determined by X-ray diffraction at 2.21 Å resolution. Released 5 Jan 2022.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,247
Mol. weight: 33.89 kDa
Ligands: PG0, ZN
Released: 5 Jan 2022

Explore 7M4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M4O contains 13 α-helices and 22 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	653-671	19
α-helix	672	1
β-strand	673-674	2	1
α-helix	675	1
β-strand	681-686	6	1
β-strand	690-692	3	2
β-strand	698-700	3	2
β-strand	706-707	2	2
α-helix	710-712	3
β-strand	713-714	2	3
α-helix	729	1
β-strand	730-731	2	3
α-helix	737-758	22

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	4
β-strand	48-49	2	4
β-strand	55	1	5
α-helix	56-59	4
β-strand	66-69	4	4
β-strand	71-74	4	1

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
β-strand	55	1	7
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-71	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF216	A	protein	138	Homo sapiens	Q9NWF9 (AlphaFold model)
Ubiquitin	B, C	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M4O_1 E3 ubiquitin-protein ligase RNF216 (chains A)
GPEELAEKDDIKYRTSIEEKMTAARIRKCHKCGTGLIKSEGANRMSCRCGAQMCYLCRVS
INGYDHFCQHPRSPGAPCQECSRCSLWTDPTEDDEKLIEEIQKEAEEEQKRKNGENTFKR
IGPPLEKPVEKVQRVEAL

Sequence of entity 2 (B, C), FASTA

>7M4O_2 Ubiquitin (chains B, C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
PG0	2-(2-methoxyethoxy)ethanol	C5 H12 O3	1
ZN	Zinc ion	Zn	3

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Cotton, T.R., Cobbold, S.A., Bernardini, J.P. et al. Mol Cell (2022) 82:598-615.e8. DOI 10.1016/j.molcel.2021.12.005 · PubMed

Other PDB entries of the same protein (UniProt Q9NWF9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M4M 2.39 Å, Crystal structure of RBR E3 ligase RNF216 with ubiquitin
7M4N 2.52 Å, Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin
8EB0 3.03 Å, RNF216/E2-Ub/Ub transthiolation complex

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