4C8T: Xenopus ZNRF3 ectodomain crystal form I

Name: PDB 4C8T: Xenopus ZNRF3 ectodomain crystal form I
Published: 2013-11-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Xenopus ZNRF3 ectodomain crystal form I. Determined by X-ray diffraction at 2.4 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: XENOPUS (SILURANA) TROPICALIS
Chains: 2
Atoms: 2,229
Mol. weight: 40.99 kDa
Released: 20 Nov 2013

Explore 4C8T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C8T contains 12 α-helices and 18 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-41	11	1
β-strand	47-58	12	1
β-strand	62	1	2
β-strand	67-74	8	1
α-helix	76-79	4
β-strand	93-98	6	1
α-helix	99-101	3
α-helix	102-104	3
α-helix	112-121	10
β-strand	124-130	7	1
α-helix	136-141	6
α-helix	147-148	2
β-strand	149	1	2
β-strand	153-156	4	1
α-helix	158-170	13
β-strand	174-179	6	1

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-41	11	3
β-strand	47-58	12	3
β-strand	62-63	2	4
β-strand	67-74	8	3
α-helix	76-79	4
β-strand	93-98	6	3
α-helix	112-121	10
β-strand	124-130	7	3
α-helix	137-141	5
α-helix	147-148	2
β-strand	149-152	4	4
β-strand	153-156	4	3
α-helix	158-168	11
β-strand	174-179	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ZNRF3	A, B	protein	182	XENOPUS (SILURANA) TROPICALIS	Q08D68 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4C8T_1 E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 (chains A, B)
ETGESLAKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCN
NNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQL
NQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRPPRQPTEYFDGTHHHHHHHH
HH

Primary citation

Structural and Molecular Basis of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition by the Wnt Agonist R-Spondin. Zebisch, M., Xu, Y., Krastev, C. et al. Nat Commun (2013) 4:2787. DOI 10.1038/NCOMMS3787 · PubMed

Other PDB entries of the same protein (UniProt Q08D68 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4C9R 2.1 Å, Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form I
4C9U 3.0 Å, Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II
4C8U 3.01 Å, Xenopus ZNRF3 ectodomain crystal form II

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