7M4M: RBR E3 ligase RNF216 with ubiquitin

Name: PDB 7M4M: Crystal structure of RBR E3 ligase RNF216 with ubiquitin
Published: 2022-01-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of RBR E3 ligase RNF216 with ubiquitin. Determined by X-ray diffraction at 2.39 Å resolution. Released 5 Jan 2022.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,959
Mol. weight: 81.25 kDa
Ligands: ZN
Released: 5 Jan 2022

Explore 7M4M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M4M contains 12 α-helices and 40 β-strands across 4 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: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	601-604	4	1
β-strand	611-614	4	1
β-strand	620-622	3	2
β-strand	631-633	3	2
β-strand	639	1	2
α-helix	641-643	3
α-helix	648-671	24
β-strand	673-674	2	3
β-strand	681-684	4	3
β-strand	690-692	3	4
β-strand	698-700	3	4
β-strand	706-707	2	4
α-helix	710-712	3
β-strand	713-714	2	5
β-strand	730-731	2	5
α-helix	737-759	23

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	602-604	3	6
β-strand	611-613	3	6
β-strand	620-622	3	7
β-strand	631-633	3	7
β-strand	639	1	7
α-helix	641-643	3
α-helix	648-671	24
β-strand	673-674	2	8
β-strand	681-684	4	8
β-strand	690-692	3	9
β-strand	698-700	3	9
β-strand	706-707	2	9
α-helix	710-712	3
β-strand	713-714	2	10
β-strand	730-731	2	10
α-helix	737-759	23

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	12-16	5	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	11
β-strand	48-49	2	11
β-strand	55	1	12
β-strand	66-69	4	11
β-strand	71-73	3	3

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	13
β-strand	12-16	5	13
β-strand	22	1	14
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	13
β-strand	48-49	2	13
β-strand	55	1	14
β-strand	66-69	4	13
β-strand	70-73	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF216	A, B	protein	277	Homo sapiens	Q9NWF9 (AlphaFold model)
Ubiquitin	C, D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7M4M_1 E3 ubiquitin-protein ligase RNF216 (chains A, B)
GPGQLIECRCCYGEFPFEELTQCADAHLFCKECLIRYAQEAVFGSGKLELSCMEGSCTCS
FPTSELEKVLPQTILYKYYERKAEEEVAAAYADELVRCPSCSFPALLDSDVKRFSCPNPH
CRKETCRKCQGLWKEHNGLTCEELAEKDDIKYRTSIEEKMTAARIRKCHKCGTGLIKSEG
CNRMSCRCGAQMCYLCRVSINGYDHFCQHPRSPGAPCQECSRCSLWTDPTEDDEKLIEEI
QKEAEEEQKRKNGENTFKRIGPPLEKPVEKVQRVEAL

Sequence of entity 2 (C, D), FASTA

>7M4M_2 Ubiquitin (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10

Water and common crystallization additives (GOL) 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:

7M4O 2.21 Å, Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked…
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

Browse structure collections

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