8G4Y: ZNRF3 ECD

Name: PDB 8G4Y: Structure of ZNRF3 ECD bound to peptide MK1-3.6.10
Published: 2023-12-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of ZNRF3 ECD bound to peptide MK1-3.6.10. Determined by X-ray diffraction at 1.41 Å resolution. Released 20 Dec 2023.

Method: X-ray diffraction
Resolution: 1.41 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,661
Mol. weight: 24.16 kDa
Released: 20 Dec 2023

Explore 8G4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G4Y contains 9 α-helices and 10 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	1
β-strand	74-85	12	1
β-strand	94-100	7	1
α-helix	103-107	5
α-helix	113-115	3
β-strand	120-125	6	1
α-helix	126-128	3
α-helix	129-131	3
α-helix	139-148	10
β-strand	151-157	7	1
α-helix	163-169	7
α-helix	174-176	3
β-strand	180-183	4	1
α-helix	185-195	11
β-strand	201-207	7	1

Chain B: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	2
α-helix	12-14	3
β-strand	20-23	4	2
β-strand	32-35	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ZNRF3	A	protein	178	Homo sapiens	Q9ULT6 (AlphaFold model)
MK1-3.6.10	B	protein	39	synthetic construct

Sequence of entity 1 (A), FASTA

>8G4Y_1 E3 ubiquitin-protein ligase ZNRF3 (chains A)
GSTKETAFVEVVLFESSPSGDYTTYTTGLTGRFSRAGATLSAEGEIVQMHPLGLCNNNDE
EDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGS
EDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHRPPRQPTEYFDMGNSDYKDDDDK

Sequence of entity 2 (B), FASTA

>8G4Y_2 MK1-3.6.10 (chains B)
GCNRLNKKCNSDADCCANKEKCERPIGWKFMYCRPDVGP

Primary citation

Potent and selective binders of the E3 ubiquitin ligase ZNRF3 stimulate Wnt signaling and intestinal organoid growth. Kschonsak, Y.T., Gao, X., Miller, S.E. et al. Cell Chem Biol (2024) 31:1176. DOI 10.1016/j.chembiol.2023.11.006 · PubMed

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

9OZX 2.4 Å, Crystal structure of ZNRF3 RING in complex with UbcH5b
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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