9Q88: RNF38 RING domain

Name: PDB 9Q88: High-resolution structure of RNF38 RING domain
Published: 2025-07-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

High-resolution structure of RNF38 RING domain. Determined by X-ray diffraction at 1.2 Å resolution. Released 30 Jul 2025.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 741
Mol. weight: 9.27 kDa
Ligands: ZN
Released: 30 Jul 2025

Explore 9Q88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q88 contains 3 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	392-394	3
α-helix	396-397	2
β-strand	398-400	3	1
β-strand	412-413	2	2
β-strand	418-419	2	2
β-strand	425-428	4	1
β-strand	434-436	3	1
α-helix	437-447	11
β-strand	449	1	3
β-strand	456	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF38	A	protein	79	Homo sapiens	Q9H0F5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9Q88_1 E3 ubiquitin-protein ligase RNF38 (chains A)
GSTKADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA
NRTCPICRADASEVHRDSE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Tuning ubiquitin transfer by RING E3 ubiquitin ligases through the linchpin residue. Nakasone, M.A., Buetow, L., Gabrielsen, M. et al. Life Sci Alliance (2025) 8. DOI 10.26508/lsa.202503394 · PubMed

Other PDB entries of the same protein (UniProt Q9H0F5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
4V3K 2.04 Å, RNF38-UbcH5B-UB complex
7OJX 2.4 Å, E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for…
9Q8Y 2.63 Å, Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub
1X4J Solution structure of RING finger in RING finger protein 38

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