4C9U: Xenopus ZNRF3 ectodomain

Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: XENOPUS (SILURANA) TROPICALIS
Chains: 4
Atoms: 3,856
Mol. weight: 68.55 kDa
Released: 20 Nov 2013

Explore 4C9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C9U contains 17 α-helices and 39 β-strands across 4 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
α-helix	26-30	5
β-strand	31-41	11	1
β-strand	47-58	12	1
β-strand	63	1	2
β-strand	67-73	7	1
α-helix	89-90	2
β-strand	93-98	6	1
α-helix	99-101	3
α-helix	112-121	10
β-strand	124-130	7	1
α-helix	136-141	6
α-helix	147-149	3
β-strand	152	1	2
β-strand	153-156	4	1
α-helix	158-170	13
β-strand	174-179	6	1

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	3
β-strand	51-55	5	3
β-strand	60-66	7	3
β-strand	69-75	7	3
α-helix	78-79	2
β-strand	82-86	5	3
β-strand	91-95	5	3
β-strand	101-106	6	4
β-strand	109-113	5	4
β-strand	118-120	3	5
β-strand	123-125	3	5
α-helix	128-129	2
α-helix	134-135	2
β-strand	140	1	5

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-41	11	6
β-strand	47-58	12	6
β-strand	63	1	7
β-strand	67-73	7	6
α-helix	86-88	3
β-strand	93-98	6	6
α-helix	112-121	10
β-strand	124-130	7	6
α-helix	136-141	6
α-helix	147-149	3
β-strand	152	1	7
β-strand	153-156	4	6
α-helix	158-170	13
β-strand	174-179	6	6

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	8
β-strand	51-55	5	8
β-strand	60-66	7	8
β-strand	69-75	7	8
α-helix	78-79	2
β-strand	82-86	5	8
β-strand	91-95	5	8
β-strand	101-104	4	9
β-strand	110-113	4	9
α-helix	114	1
β-strand	120	1	10
β-strand	123	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ZNRF3	A, C	protein	182	XENOPUS (SILURANA) TROPICALIS	Q08D68 (AlphaFold model)
R-spondin-2	B, D	protein	121	XENOPUS (SILURANA) TROPICALIS	Q5M7L6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4C9U_1 E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 (chains A, C)
ETGESLAKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCN
NNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQL
NQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRPPRQPTEYFDGTHHHHHHHH
HH

Sequence of entity 2 (B, D), FASTA

>4C9U_2 R-SPONDIN-2 (chains B, D)
ETGGTNPICKGCLSCSKDNGCLRCQPKLFFYLRREGMRQYGECLQSCPPGYYGVRGPDMN
RCSRCRIENCDSCFSRDFCIKCKSGFYSHKGQCFEECPEGFAPLDDTMVCVDGTKHHHHH
H

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
4C8U 3.01 Å, Xenopus ZNRF3 ectodomain crystal form II

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