4C9A: Mouse ZNRF3 ectodomain

Name: PDB 4C9A: Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form I
Published: 2013-11-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) 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
Organisms: MUS MUSCULUS, XENOPUS (SILURANA) TROPICALIS
Chains: 4
Atoms: 3,815
Mol. weight: 64.25 kDa
Released: 20 Nov 2013

Explore 4C9A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C9A contains 16 α-helices and 42 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	55-65	11	1
β-strand	71-82	12	1
β-strand	91-97	7	1
α-helix	100-102	3
β-strand	118-122	5	1
α-helix	123-125	3
α-helix	126-128	3
α-helix	136-145	10
β-strand	150-154	5	1
α-helix	160-166	7
β-strand	177-180	4	1
α-helix	182-194	13
β-strand	199-204	6	1

Chain B: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	2
β-strand	46-47	2	3
β-strand	51-52	2	3
β-strand	55	1	2
β-strand	60-66	7	3
β-strand	69-75	7	3
α-helix	78-79	2
β-strand	82-83	2	4
β-strand	92	1	3
β-strand	94-95	2	4
β-strand	101	1	5
β-strand	104	1	6
β-strand	110	1	6
β-strand	113	1	5
α-helix	114	1
β-strand	119	1	7
β-strand	120	1	8
β-strand	123	1	8
α-helix	134-135	2
β-strand	140	1	7

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	55-65	11	9
β-strand	71-82	12	9
β-strand	91-97	7	9
α-helix	100-102	3
α-helix	113-114	2
β-strand	117-122	6	9
α-helix	123-125	3
α-helix	136-145	10
β-strand	148-154	7	9
α-helix	161-166	6
β-strand	177-180	4	9
α-helix	182-194	13
β-strand	199-203	5	9

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	10
β-strand	51-55	5	10
β-strand	60-66	7	10
β-strand	69-75	7	10
α-helix	78-79	2
β-strand	82-84	3	11
β-strand	91-92	2	10
β-strand	93-95	3	11
β-strand	101-106	6	12
β-strand	109-113	5	12
β-strand	118-120	3	13
β-strand	123-125	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ZNRF3	A, C	protein	165	MUS MUSCULUS	Q5SSZ7 (AlphaFold model)
R-spondin-2	B, D	protein	121	XENOPUS (SILURANA) TROPICALIS	Q5M7L6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4C9A_1 E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 (chains A, C)
ETGKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDE
EDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGS
EDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHLGTKHHHHHH

Sequence of entity 2 (B, D), FASTA

>4C9A_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 Q5SSZ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CDJ 1.5 Å, Structure of ZNRF3 ectodomain
4C86 2.0 Å, mouse ZNRF3 ectodomain crystal form I
4C8P 2.1 Å, mouse ZNRF3 ectodomain crystal form V, disulfide-bridged S90C variant
4C8C 2.4 Å, mouse ZNRF3 ectodomain crystal form III
4C8F 2.69 Å, mouse ZNRF3 ectodomain crystal form IV
4C8A 2.7 Å, mouse ZNRF3 ectodomain crystal form II
4C99 2.8 Å, Mouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crystal form I
4CDK 2.8 Å, Structure of ZNRF3-RSPO1
4C9E 3.0 Å, Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II

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