9KB9: LGR4-RSPO2-ZNRF3 complex

Cryo-EM structure of LGR4-RSPO2-ZNRF3 complex (2:2:2). Determined by electron microscopy at 3.59 Å resolution. Released 15 Oct 2025.

Method: Electron microscopy
Resolution: 3.59 Å
Organism: Homo sapiens
Chains: 6
Atoms: 16,352
Mol. weight: 277.31 kDa
Ligands: NAG
Released: 15 Oct 2025

Explore 9KB9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KB9 contains 60 α-helices and 108 β-strands across 6 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: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	1
β-strand	40-42	3	1
β-strand	61-63	3	1
β-strand	71-72	2	2
β-strand	85-87	3	1
β-strand	95-96	2	2
β-strand	109-111	3	1
β-strand	119	1	3
β-strand	133-135	3	1
β-strand	143	1	3
β-strand	157-159	3	1
α-helix	170-173	4
β-strand	181-183	3	1
β-strand	191-192	2	4
β-strand	205-207	3	1
β-strand	215-216	2	4
β-strand	229-231	3	1
α-helix	242-246	5
β-strand	252-254	3	1
β-strand	262-263	2	5
β-strand	276-278	3	1
β-strand	286-287	2	5
β-strand	300-304	5	6
α-helix	312-314	3
β-strand	323-327	5	6
α-helix	338-341	4
β-strand	347-349	3	6
α-helix	358-360	3
β-strand	369-371	3	6
β-strand	379-380	2	7
α-helix	382-385	4
β-strand	393-395	3	6
β-strand	403-404	2	7
β-strand	417-419	3	6
β-strand	438-440	3	6
α-helix	453-455	3
β-strand	461-463	3	6
α-helix	467-470	4
β-strand	521	1	6
α-helix	539-564	26
α-helix	572-600	29
α-helix	605-614	10
α-helix	616-652	37
α-helix	659-682	24
α-helix	687-689	3
α-helix	701-731	31
α-helix	733-737	5
α-helix	741-772	32
α-helix	779-789	11
α-helix	792-795	4
α-helix	797-803	7
α-helix	806-821	16

Chain B: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	10
β-strand	46-47	2	11
β-strand	51-52	2	11
β-strand	55	1	10
β-strand	60-66	7	11
β-strand	69-75	7	11
β-strand	82-85	4	11
β-strand	91-95	5	11
β-strand	101-104	4	12
β-strand	110-113	4	12
β-strand	118-120	3	13
β-strand	123-125	3	13
β-strand	133	1	14
β-strand	142	1	14

Chain C: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	8
β-strand	74-85	12	8
β-strand	89	1	9
β-strand	94-101	8	8
α-helix	103-105	3
α-helix	111-113	3
α-helix	116-117	2
β-strand	120-125	6	8
α-helix	129-131	3
α-helix	139-148	10
β-strand	151-157	7	8
α-helix	163-169	7
β-strand	176	1	9
β-strand	180-183	4	8
α-helix	186-195	10
β-strand	201-207	7	8
α-helix	208-210	3
α-helix	214-216	3
α-helix	218-245	28

Chain D: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	15
β-strand	40-42	3	15
β-strand	61-63	3	15
β-strand	71-72	2	16
β-strand	85-87	3	15
β-strand	95-96	2	16
β-strand	109-111	3	15
β-strand	119	1	17
β-strand	133-135	3	15
β-strand	143	1	17
β-strand	157-159	3	15
α-helix	170-174	5
β-strand	181-183	3	15
β-strand	191-192	2	18
β-strand	205-207	3	15
β-strand	215-216	2	18
β-strand	229-231	3	15
α-helix	242-246	5
β-strand	252-254	3	15
β-strand	262-263	2	19
β-strand	276-278	3	15
β-strand	286-287	2	19
β-strand	302-304	3	20
β-strand	323-327	5	20
α-helix	338-341	4
β-strand	347-349	3	20
α-helix	358-360	3
β-strand	369-371	3	20
β-strand	379-380	2	21
α-helix	382-385	4
β-strand	393-395	3	20
β-strand	403-404	2	21
β-strand	417-419	3	20
β-strand	438-440	3	20
α-helix	453-455	3
β-strand	461-463	3	20
α-helix	467-470	4
β-strand	521	1	20
α-helix	542-564	23
α-helix	572-600	29
α-helix	605-614	10
α-helix	616-651	36
α-helix	659-678	20
α-helix	679-683	5
α-helix	687-689	3
α-helix	701-731	31
α-helix	733-737	5
α-helix	742-772	31
α-helix	779-789	11
α-helix	792-795	4
α-helix	797-803	7
α-helix	806-821	16

Chain E: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	22
β-strand	74-85	12	22
β-strand	89	1	23
β-strand	94-101	8	22
α-helix	103-105	3
α-helix	111-114	4
α-helix	116-117	2
β-strand	120-125	6	22
α-helix	129-131	3
α-helix	139-148	10
β-strand	151-157	7	22
α-helix	163-169	7
β-strand	176	1	23
β-strand	180-183	4	22
α-helix	186-195	10
β-strand	202-207	6	22
α-helix	215-245	31

Chain F: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	24
β-strand	46-47	2	25
β-strand	51-52	2	25
β-strand	55	1	24
β-strand	60-66	7	25
β-strand	69-75	7	25
β-strand	82-85	4	25
β-strand	91-95	5	25
β-strand	101-104	4	26
β-strand	110-113	4	26
β-strand	118-120	3	27
β-strand	123-125	3	27
β-strand	133-135	3	28
β-strand	140-142	3	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A, D	protein	845	Homo sapiens	Q9BXB1 (AlphaFold model)
E3 ubiquitin-protein ligase ZNRF3	C, E	protein	231	Homo sapiens	Q9ULT6 (AlphaFold model)
R-spondin-2	B, F	protein	160	Homo sapiens	Q6UXX9 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9KB9_1 Leucine-rich repeat-containing G-protein coupled receptor 4 (chains A, D)
MPGPLGLLCFLALGLLGSAGPSGAAPPLCAAPCSCDGDRRVDCSGKGLTAVPEGLSAFTQ
ALDISMNNITQLPEDAFKNFPFLEELQLAGNDLSFIHPKALSGLKELKVLTLQNNQLKTV
PSEAIRGLSALQSLRLDANHITSVPEDSFEGLVQLRHLWLDDNSLTEVPVHPLSNLPTLQ
ALTLALNKISSIPDFAFTNLSSLVVLHLHNNKIRSLSQHCFDGLDNLETLDLNYNNLGEF
PQAIKALPSLKELGFHSNSISVIPDGAFDGNPLLRTIHLYDNPLSFVGNSAFHNLSDLHS
LVIRGASMVQQFPNLTGTVHLESLTLTGTKISSIPNNLCQEQKMLRTLDLSYNNIRDLPS
FNGCHALEEISLQRNQIYQIKEGTFQGLISLRILDLSRNLIHEIHSRAFATLGPITNLDV
SFNELTSFPTEGLNGLNQLKLVGNFKLKEALAAKDFVNLRSLSVPYAYQCCAFWGCDSYA
NLNTEDNSLQDHSVAQEKGTADAANVTSTLENEEHSQIIIHCTPSTGAFKPCEYLLGSWM
IRLTVWFIFLVALFFNLLVILTTFASCTSLPSSKLFIGLISVSNLFMGIYTGILTFLDAV
SWGRFAEFGIWWETGSGCKVAGFLAVFSSESAIFLLMLATVERSLSAKDIMKNGKSNHLK
QFRVAALLAFLGATVAGCFPLFHRGEYSASPLCLPFPTGETPSLGFTVTLVLLNSLAFLL
MAVIYTKLYCNLEKEDLSENSQSSMIKHVAWLIFTNCIFFCPVAFFSFAPLITAISISPE
IMKSVTLIFFPLPACLNPVLYVFFNPKFKEDWKLLKRRVTKKENLYFQGDYKDDDDKHHH
HHHHH

Sequence of entity 2 (C, E), FASTA

>9KB9_2 E3 ubiquitin-protein ligase ZNRF3 (chains C, E)
METGLRWLLLVAVLKGVQCKETAFVEVVLFESSPSGDYTTYTTGLTGRFSRAGATLSAEG
EIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIF
DVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHRPPRQPTEY
FDMGIFLAFFVVVSLVCLILLVKIKLKQRRSQNSMNRLAVQALEKMETRKF

Sequence of entity 3 (B, F), FASTA

>9KB9_3 R-spondin-2 (chains B, F)
MQFRLFSFALIILNCMDYSHCQGNRWRRSKRASYVSNPICKGCLSCSKDNGCSRCQQKLF
FFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLH
RGRCFDECPDGFAPLEETMECVEENLYFQGHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural insights into Wnt/ beta-catenin signaling regulation by LGR4, R-spondin, and ZNRF3. Peng, Y., Fujimura, A., Asami, J. et al. Nat Commun (2025) 16:8337-8337. DOI 10.1038/s41467-025-64129-z · PubMed

Other PDB entries of the same protein (UniProt Q9BXB1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QXE 2.2 Å, Crystal structure of LGR4 fused with hagfish VLR
4QXF 2.25 Å, crystal structure of human LGR4 and Rspo1
4KT1 2.5 Å, Complex of R-spondin 1 with LGR4 extracellular domain
9KGK 2.63 Å, Structure of the complex of LGR4 with NB18
8XUM 2.9 Å, Structure of LGR4 with RSPO2
9UOK 3.05 Å, Structure of the complex of LGR4_ECD with Norrin
8XT9 3.1 Å, structure of LGR4
8XFS 3.2 Å, LGR4-RSPO2-ZNRF3 RING domain (1:2:2)
8XFP 3.21 Å, the pentamerA complex of LGR4-RSPO2-ZNRF3(delta RING)
8XFT 3.24 Å, LGR4-RSPO2-ZNRF3(1:1:1)
9KB8 3.25 Å, Cryo-EM structure of LGR4-RSPO2-ZNRF3 complex (1:1:2)
8WVY 3.29 Å, Cryo-EM structure of LGR4 in complex with Norrin

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