4C8U: Xenopus ZNRF3 ectodomain crystal form II

Name: PDB 4C8U: Xenopus ZNRF3 ectodomain crystal form II
Published: 2013-11-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Xenopus ZNRF3 ectodomain crystal form II. Determined by X-ray diffraction at 3.01 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 3.01 Å
Organism: XENOPUS (SILURANA) TROPICALIS
Chains: 2
Atoms: 2,207
Mol. weight: 41.07 kDa
Released: 20 Nov 2013

Explore 4C8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C8U contains 13 α-helices and 22 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	67-72	6	1
α-helix	76-78	3
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	137-142	6
α-helix	147-148	2
β-strand	149	1	2
β-strand	154-156	3	1
α-helix	158-170	13
β-strand	174-179	6	1

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	3
β-strand	33-37	5	4
β-strand	40-41	2	5
β-strand	47-48	2	5
β-strand	53	1	4
β-strand	56-58	3	3
β-strand	67	1	4
β-strand	70	1	4
β-strand	71-74	4	6
α-helix	76-78	3
β-strand	93-97	5	6
α-helix	102-104	3
α-helix	112-121	10
β-strand	124-128	5	6
α-helix	137-141	5
α-helix	147-149	3
β-strand	154-155	2	3
α-helix	158-168	11
β-strand	175-179	5	4

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

>4C8U_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
4C8T 2.4 Å, Xenopus ZNRF3 ectodomain crystal form I
4C9U 3.0 Å, Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II

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