8EB0: RNF216/E2-Ub/Ub transthiolation complex

Name: PDB 8EB0: RNF216/E2-Ub/Ub transthiolation complex
Published: 2023-01-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

RNF216/E2-Ub/Ub transthiolation complex. Determined by X-ray diffraction at 3.03 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,423
Mol. weight: 67.58 kDa
Ligands: ZN
Released: 18 Jan 2023

Explore 8EB0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EB0 contains 23 α-helices and 39 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: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	513-514	2	1
α-helix	515	1
β-strand	521-522	2	1
α-helix	524-526	3
β-strand	527-529	3	2
β-strand	535-537	3	2
α-helix	538-549	12
β-strand	558	1	3
β-strand	567	1	3
α-helix	570-576	7
α-helix	579-598	20
β-strand	602-604	3	4
β-strand	611-613	3	4
β-strand	620-622	3	5
β-strand	631-633	3	5
β-strand	638-639	2	5
α-helix	640-643	4
α-helix	648-653	6
α-helix	656-669	14
β-strand	673-674	2	6
β-strand	681-684	4	6
β-strand	690-692	3	7
β-strand	698-700	3	7
α-helix	710-712	3
β-strand	713	1	8
α-helix	729	1
β-strand	730	1	8
α-helix	731	1
α-helix	737-757	21

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-16	15
β-strand	22-27	6	9
β-strand	34-39	6	9
β-strand	51-56	6	9
β-strand	67-70	4	9
β-strand	79	1	10
β-strand	84	1	9
β-strand	85	1	10
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-145	13

Chain C: 3 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	43-44	2	11
β-strand	49	1	11
β-strand	55	1	12
α-helix	56-59	4
β-strand	66-69	4	11
β-strand	71-73	3	6

Chain D: 3 helices, 7 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	41-45	5	13
β-strand	48-49	2	13
α-helix	50-51	2
β-strand	55	1	14
β-strand	66-71	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF216	A	protein	277	Homo sapiens	Q9NWF9 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	B	protein	157	Homo sapiens	P68036 (AlphaFold model)
Ubiquitin	C, D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8EB0_1 E3 ubiquitin-protein ligase RNF216 (chains A)
GPGQLIECRCCYGEFPFEELTQCADAHLFCKECLIRYAQEAVFGSGKLELSCMEGSCTCS
FPTSELEKVLPQTILYKYYERKAEEEVAAAYADELVRCPSCSFPALLDSDVKRFSCPNPH
CRKETCRKCQGLWKEHNGLTCEELAEKDDIKYRTSIEEKMTAARIRKCHKCGTGLIKSEG
ANRMSCRCGAQMCYLCRVSINGYDHFCQHPRSPGAPCQECSRCSLWTDPTEDDEKLIEEI
QKEAEEEQKRKNGENTFKRIGPPLEKPVEKVQRVEAL

Sequence of entity 2 (B), FASTA

>8EB0_2 Ubiquitin-conjugating enzyme E2 L3 (chains B)
GPGMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINF
PAEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQP
EHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Sequence of entity 3 (C, D), FASTA

>8EB0_3 Ubiquitin (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

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

Primary citation

The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family. Wang, X.S., Cotton, T.R., Trevelyan, S.J. et al. Nat Commun (2023) 14:168-168. DOI 10.1038/s41467-023-35871-z · 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…
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

Browse structure collections

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