8GCB: RNF125

Name: PDB 8GCB: Structure of RNF125 in complex with a UbcH5b~Ub conjugate
Published: 2023-07-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of RNF125 in complex with a UbcH5b~Ub conjugate. Determined by X-ray diffraction at 2.39 Å resolution. Released 19 Jul 2023.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,936
Mol. weight: 28.76 kDa
Ligands: ZN
Released: 19 Jul 2023

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

Secondary structure: helices and β-sheets

8GCB contains 13 α-helices and 17 β-strands across 2 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	21-26	6	1
β-strand	29-38	10	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	3
β-strand	43	1	3
α-helix	44	1
β-strand	47-49	3	4
β-strand	55-57	3	4
α-helix	58-67	10
β-strand	71	1	5
β-strand	78	1	5
β-strand	84-85	2	4
α-helix	87-93	7
β-strand	97-99	3	6
β-strand	106-108	3	6
α-helix	109-111	3
α-helix	112-117	6
α-helix	120-125	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	152	Homo sapiens	P62837 (AlphaFold model)
E3 ubiquitin-protein ligase RNF125	B	protein	101	Homo sapiens	Q96EQ8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8GCB_1 Ubiquitin-conjugating enzyme E2 D2 (chains A)
GPLGSMALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIH
FPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNP
DDPLVPEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (B), FASTA

>8GCB_2 E3 ubiquitin-protein ligase RNF125 (chains B)
GPLGSVTSFDCAVCLEVLHQPVRTRCGHVFCRSCIATSLKNNKWTCPYCRAYLPSEGVPA
TDVAKRMKSEYKNCAECDTLVCLSEMRAHIRTCQKYIDKYG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Zinc finger 1 of the RING E3 ligase, RNF125, interacts with the E2 to enhance ubiquitylation. Middleton, A.J., Barzak, F.M., Fokkens, T.J. et al. Structure (2023) 31:1208-1219.e5. DOI 10.1016/j.str.2023.07.007 · PubMed

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub

Browse structure collections

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