4CDK: ZNRF3-RSPO1

Structure of ZNRF3-RSPO1. Determined by X-ray diffraction at 2.8 Å resolution. Released 8 Jan 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS
Chains: 8
Atoms: 7,982
Mol. weight: 126.77 kDa
Released: 8 Jan 2014

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

Secondary structure: helices and β-sheets

4CDK contains 30 α-helices and 83 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: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	1
α-helix	73	1
β-strand	74-85	12	1
β-strand	89	1	2
β-strand	94-100	7	1
α-helix	103-106	4
α-helix	111-113	3
β-strand	120-125	6	1
α-helix	126-128	3
α-helix	139-148	10
β-strand	151-157	7	1
α-helix	163-169	7
α-helix	174-175	2
β-strand	176	1	2
β-strand	180-183	4	1
α-helix	185-197	13
β-strand	202-206	5	1

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	59-68	10	3
α-helix	73	1
β-strand	74-83	10	3
β-strand	84-85	2	4
β-strand	89	1	5
β-strand	94-97	4	3
β-strand	98-100	3	4
α-helix	103-106	4
β-strand	120-125	6	4
α-helix	126-128	3
α-helix	139-148	10
β-strand	151-157	7	4
α-helix	164-168	5
α-helix	169-171	3
β-strand	176	1	5
β-strand	180-183	4	4
α-helix	185-197	13
β-strand	202-207	6	3

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	1
α-helix	73	1
β-strand	74-85	12	1
β-strand	89	1	6
β-strand	94-100	7	1
α-helix	103-106	4
β-strand	120-125	6	1
α-helix	126-128	3
α-helix	139-148	10
β-strand	151-157	7	1
α-helix	163-169	7
β-strand	176	1	6
β-strand	180-183	4	1
α-helix	185-197	13
β-strand	202-206	5	1

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	7
α-helix	73	1
β-strand	74-85	12	7
β-strand	89	1	8
β-strand	94-100	7	7
α-helix	103-106	4
β-strand	120-125	6	7
α-helix	126-128	3
α-helix	129-131	3
α-helix	139-148	10
β-strand	151-157	7	7
α-helix	163-168	6
β-strand	176	1	8
β-strand	180-183	4	7
α-helix	185-197	13
β-strand	202-207	6	7

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	9
β-strand	52-56	5	9
β-strand	61-67	7	9
β-strand	70-76	7	9
α-helix	79-80	2
β-strand	83-87	5	9
β-strand	92-96	5	9
β-strand	102-104	3	10
β-strand	113-114	2	10
β-strand	119-121	3	11
β-strand	124-126	3	11
α-helix	129-130	2
β-strand	141	1	11

Chain F: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	12
β-strand	52-56	5	12
β-strand	61-67	7	12
β-strand	70-76	7	12
β-strand	83-84	2	13
β-strand	88	1	14
β-strand	91	1	14
β-strand	93	1	12
β-strand	95-96	2	13
β-strand	102-104	3	15
β-strand	113-114	2	15
β-strand	119-121	3	16
β-strand	124-126	3	16

Chain G: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	17
β-strand	52-56	5	17
β-strand	61-67	7	17
β-strand	70-76	7	17
β-strand	83-86	4	17
β-strand	93-96	4	17
β-strand	102-104	3	18
β-strand	113-114	2	18
β-strand	119-121	3	19
β-strand	124-126	3	19

Chain H: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	20
β-strand	52-56	5	20
β-strand	61-67	7	20
β-strand	70-76	7	20
β-strand	83-84	2	21
β-strand	92-93	2	20
β-strand	95-96	2	21
β-strand	104	1	22
β-strand	113	1	22
β-strand	119-121	3	23
β-strand	124-126	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ZNRF3	A, B, C, D	protein	164	MUS MUSCULUS	Q5SSZ7 (AlphaFold model)
R-spondin-1	E, F, G, H	protein	126	HOMO SAPIENS	Q2MKA7 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4CDK_1 E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 (chains A, B, C, D)
GSKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEE
DLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSE
DPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHLAAAHHHHHH

Sequence of entity 2 (E, F, G, H), FASTA

>4CDK_2 R-SPONDIN-1 (chains E, F, G, H)
GSRISAEGSQACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARN
PDMNKCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGSSAANGTMECSSPAAA
HHHHHH

Primary citation

Structures of Wnt-Antagonist Znrf3 and its Complex with R-Spondin 1 and Implications for Signaling. Peng, W.C., De Lau, W., Madoori, P.K. et al. PLoS One (2013) 8:83110. DOI 10.1371/JOURNAL.PONE.0083110 · 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
4C9E 3.0 Å, Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II

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