4C9R: Xenopus ZNRF3 ectodomain

Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form I. Determined by X-ray diffraction at 2.1 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: XENOPUS (SILURANA) TROPICALIS
Chains: 4
Atoms: 4,365
Mol. weight: 68.55 kDa
Released: 20 Nov 2013

Explore 4C9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C9R contains 20 α-helices and 40 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-30	6
β-strand	31-41	11	1
β-strand	47-58	12	1
β-strand	67-73	7	1
α-helix	76-78	3
α-helix	89-90	2
β-strand	93-98	6	1
α-helix	102-104	3
α-helix	112-121	10
β-strand	124-130	7	1
α-helix	136-142	7
α-helix	147-149	3
β-strand	153-156	4	1
α-helix	158-170	13
β-strand	175-179	5	1

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	2
β-strand	51-55	5	2
β-strand	60-66	7	2
β-strand	69-75	7	2
α-helix	78-79	2
β-strand	82-86	5	2
β-strand	91-95	5	2
β-strand	101-106	6	3
β-strand	109-113	5	3
α-helix	117	1
β-strand	118-120	3	4
β-strand	123-125	3	4
α-helix	128-129	2
β-strand	133-134	2	5
β-strand	140	1	4
β-strand	141-142	2	5

Chain C: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
β-strand	31-41	11	6
β-strand	47-58	12	6
β-strand	67-73	7	6
α-helix	76-78	3
β-strand	93-98	6	6
α-helix	99-101	3
α-helix	102-104	3
α-helix	112-121	10
β-strand	124-130	7	6
α-helix	136-141	6
α-helix	147-149	3
β-strand	153-156	4	6
α-helix	158-170	13
β-strand	175-179	5	6

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	7
β-strand	51-55	5	7
β-strand	60-66	7	7
β-strand	69-75	7	7
α-helix	78-79	2
β-strand	82-86	5	7
β-strand	91-95	5	7
β-strand	101-104	4	8
β-strand	110-113	4	8
β-strand	118-120	3	9
β-strand	123-125	3	9
β-strand	132-134	3	10
β-strand	140	1	9
β-strand	141-143	3	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

>4C9R_1 E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 (chains A, C)
ETGESLAKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCN
NNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQL
NQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRPPRQPTEYFDGTHHHHHHHH
HH

Sequence of entity 2 (B, D), FASTA

>4C9R_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:

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
4C8U 3.01 Å, Xenopus ZNRF3 ectodomain crystal form II

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