4C9E: Mouse ZNRF3 ectodomain

Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) 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
Organisms: MUS MUSCULUS, XENOPUS (SILURANA) TROPICALIS
Chains: 8
Atoms: 7,644
Mol. weight: 128.13 kDa
Released: 20 Nov 2013

Explore 4C9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C9E contains 32 α-helices and 89 β-strands across 8 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	55-65	11	1
β-strand	71-82	12	1
β-strand	86	1	2
β-strand	91-98	8	1
α-helix	100-102	3
β-strand	117-122	6	1
α-helix	126-128	3
α-helix	136-145	10
β-strand	150-154	5	1
α-helix	160-166	7
α-helix	167-169	3
β-strand	173	1	2
β-strand	177-180	4	1
α-helix	182-194	13
β-strand	199-203	5	1

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	3
β-strand	46-47	2	4
β-strand	51-52	2	4
β-strand	55	1	3
β-strand	60-66	7	4
β-strand	69-75	7	4
β-strand	82-85	4	4
β-strand	92-95	4	4
β-strand	101-104	4	5
β-strand	110-113	4	5
α-helix	114	1
β-strand	118-120	3	6
β-strand	123-125	3	6
α-helix	128-129	2
α-helix	134-135	2
β-strand	140	1	6

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	55-65	11	7
β-strand	71-82	12	7
β-strand	86-87	2	8
β-strand	91-98	8	7
α-helix	100-102	3
α-helix	111-114	4
β-strand	117-122	6	7
α-helix	136-145	10
β-strand	148-154	7	7
α-helix	161-165	5
α-helix	166-170	5
β-strand	173-176	4	8
β-strand	177-180	4	7
α-helix	182-194	13
β-strand	199-203	5	7

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	9
β-strand	51-55	5	9
β-strand	60-66	7	9
β-strand	69-75	7	9
β-strand	82-86	5	9
β-strand	91-95	5	9
β-strand	101-106	6	10
β-strand	109-113	5	10
α-helix	114	1
β-strand	118-120	3	11
β-strand	123-125	3	11
β-strand	140	1	11

Chain E: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	55-65	11	12
β-strand	71-82	12	12
β-strand	86	1	13
β-strand	91-97	7	12
α-helix	100-102	3
α-helix	110-112	3
β-strand	117-122	6	12
α-helix	136-145	10
β-strand	148-154	7	12
α-helix	161-166	6
α-helix	167-169	3
β-strand	173	1	13
β-strand	177-180	4	12
α-helix	182-194	13
β-strand	199-203	5	12

Chain F: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	14
β-strand	46-47	2	15
β-strand	51-52	2	15
β-strand	55	1	14
β-strand	60-66	7	15
β-strand	69-75	7	15
α-helix	78-79	2
β-strand	82-83	2	16
β-strand	92	1	15
β-strand	94-95	2	16
β-strand	101	1	17
β-strand	104	1	18
β-strand	110	1	18
β-strand	113	1	17
α-helix	114	1
β-strand	118-120	3	19
β-strand	123-125	3	19
β-strand	130	1	20
β-strand	132	1	20
α-helix	134-135	2
β-strand	140	1	19

Chain G: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	55-65	11	21
β-strand	71-83	13	21
β-strand	86	1	22
β-strand	91-98	8	21
α-helix	100-102	3
β-strand	117-122	6	21
α-helix	123-125	3
α-helix	136-145	10
β-strand	148-154	7	21
α-helix	161-166	6
β-strand	173	1	22
β-strand	177-180	4	21
α-helix	183-194	12
β-strand	199-204	6	21

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	23
β-strand	51-55	5	23
β-strand	60-66	7	23
β-strand	69-75	7	23
α-helix	78-79	2
β-strand	82-85	4	23
β-strand	91-95	5	23
β-strand	101-106	6	24
β-strand	109-113	5	24
α-helix	117	1
β-strand	118-120	3	25
β-strand	123-125	3	25
β-strand	140	1	25

Molecules and chains

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

Sequence of entity 1 (A, C, E, G), FASTA

>4C9E_1 E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 (chains A, C, E, G)
ETGKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDE
EDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGS
EDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHLGTKHHHHHH

Sequence of entity 2 (B, D, F, H), FASTA

>4C9E_2 R-SPONDIN-2 (chains B, D, F, H)
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
4C9A 2.4 Å, Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form I
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

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