9OZX: ZNRF3 RING

Crystal structure of ZNRF3 RING in complex with UbcH5b. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Jun 2026.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,846
Mol. weight: 28.27 kDa
Ligands: ZN
Released: 17 Jun 2026

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

Secondary structure: helices and β-sheets

9OZX contains 11 α-helices and 12 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	255-261	7
β-strand	263-266	4	1
β-strand	305-308	4	1
β-strand	314-316	3	1
α-helix	317-327	11
β-strand	329	1	2
β-strand	336	1	2

Chain B: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	17-18	2
β-strand	21-26	6	3
β-strand	29-38	10	3
α-helix	39-40	2
β-strand	49-55	7	3
α-helix	60-62	3
α-helix	64-65	2
β-strand	66-69	4	3
β-strand	78	1	4
β-strand	83	1	3
β-strand	84	1	4
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ZNRF3	A	protein	97	Homo sapiens	Q9ULT6 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D2	B	protein	151	Homo sapiens	P62837 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OZX_1 E3 ubiquitin-protein ligase ZNRF3 (chains A)
QGPGNSMNRLAVQALEKMETRKFNSKSKGRREGSCGALDTLSSSSTSDCAICLEKYIDGE
ELRVIPCTHRFHRKCVDPWLLQHHTCPHCRHNIIEQK

Sequence of entity 2 (B), FASTA

>9OZX_2 Ubiquitin-conjugating enzyme E2 D2 (chains B)
QGPGMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHF
PTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPD
DPLVPEIARIYKTDREKYNRIAREWTQKYAM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Crystal structure of ZNRF3 RING in complex with UbcH5b. Padala, P., Rossig, C., Middleton, A.J. et al. To be published.

Other PDB entries of the same protein (UniProt Q9ULT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G4Y 1.41 Å, Structure of ZNRF3 ECD bound to peptide MK1-3.6.10
8XFS 3.2 Å, LGR4-RSPO2-ZNRF3 RING domain (1:2:2)
8XFP 3.21 Å, the pentamerA complex of LGR4-RSPO2-ZNRF3(delta RING)
8XFT 3.24 Å, LGR4-RSPO2-ZNRF3(1:1:1)
9KB8 3.25 Å, Cryo-EM structure of LGR4-RSPO2-ZNRF3 complex (1:1:2)
8Y69 3.38 Å, LGR4-RSPO2-ZNRF3 (2:2:2)
9KB9 3.59 Å, Cryo-EM structure of LGR4-RSPO2-ZNRF3 complex (2:2:2)
4UFS 4.8 Å, Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5…

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