9KB7: LGR4-RSPO2 complex

Cryo-EM structure of LGR4-RSPO2 complex. Determined by electron microscopy at 3.97 Å resolution. Released 15 Oct 2025.

Method: Electron microscopy
Resolution: 3.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,706
Mol. weight: 112.33 kDa
Released: 15 Oct 2025

Explore 9KB7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KB7 contains 20 α-helices and 46 β-strands across 2 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: 20 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	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	187	1	4
β-strand	191-192	2	5
β-strand	205-207	3	1
β-strand	211	1	4
β-strand	215-216	2	5
β-strand	229-231	3	1
α-helix	243-246	4
β-strand	252-254	3	1
β-strand	262-263	2	6
β-strand	276-278	3	1
β-strand	286-287	2	6
β-strand	300-303	4	7
α-helix	312-314	3
β-strand	323-326	4	7
α-helix	338-341	4
β-strand	347-349	3	7
β-strand	369-371	3	7
β-strand	379-380	2	8
α-helix	382-385	4
β-strand	393-395	3	7
β-strand	403-404	2	8
β-strand	417-419	3	7
β-strand	438-440	3	7
α-helix	453-455	3
β-strand	461-463	3	7
α-helix	467-471	5
β-strand	521-523	3	7
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	734-737	4
α-helix	741-758	18
α-helix	760-767	8
α-helix	779-789	11
α-helix	792-803	12
α-helix	806-821	16

Chain B: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43-46	4	9
β-strand	51	1	10
β-strand	52-55	4	9
β-strand	60-66	7	10
β-strand	69-75	7	10
β-strand	82-85	4	10
β-strand	91-95	5	10
β-strand	101-104	4	11
β-strand	110-113	4	11
β-strand	118-120	3	12
β-strand	123-125	3	12
β-strand	133-135	3	13
β-strand	140-142	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A	protein	845	Homo sapiens	Q9BXB1 (AlphaFold model)
R-spondin-2	B	protein	160	Homo sapiens	Q6UXX9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KB7_1 Leucine-rich repeat-containing G-protein coupled receptor 4 (chains A)
MPGPLGLLCFLALGLLGSAGPSGAAPPLCAAPCSCDGDRRVDCSGKGLTAVPEGLSAFTQ
ALDISMNNITQLPEDAFKNFPFLEELQLAGNDLSFIHPKALSGLKELKVLTLQNNQLKTV
PSEAIRGLSALQSLRLDANHITSVPEDSFEGLVQLRHLWLDDNSLTEVPVHPLSNLPTLQ
ALTLALNKISSIPDFAFTNLSSLVVLHLHNNKIRSLSQHCFDGLDNLETLDLNYNNLGEF
PQAIKALPSLKELGFHSNSISVIPDGAFDGNPLLRTIHLYDNPLSFVGNSAFHNLSDLHS
LVIRGASMVQQFPNLTGTVHLESLTLTGTKISSIPNNLCQEQKMLRTLDLSYNNIRDLPS
FNGCHALEEISLQRNQIYQIKEGTFQGLISLRILDLSRNLIHEIHSRAFATLGPITNLDV
SFNELTSFPTEGLNGLNQLKLVGNFKLKEALAAKDFVNLRSLSVPYAYQCCAFWGCDSYA
NLNTEDNSLQDHSVAQEKGTADAANVTSTLENEEHSQIIIHCTPSTGAFKPCEYLLGSWM
IRLTVWFIFLVALFFNLLVILTTFASCTSLPSSKLFIGLISVSNLFMGIYTGILTFLDAV
SWGRFAEFGIWWETGSGCKVAGFLAVFSSESAIFLLMLATVERSLSAKDIMKNGKSNHLK
QFRVAALLAFLGATVAGCFPLFHRGEYSASPLCLPFPTGETPSLGFTVTLVLLNSLAFLL
MAVIYTKLYCNLEKEDLSENSQSSMIKHVAWLIFTNCIFFCPVAFFSFAPLITAISISPE
IMKSVTLIFFPLPACLNPVLYVFFNPKFKEDWKLLKRRVTKKENLYFQGDYKDDDDKHHH
HHHHH

Sequence of entity 2 (B), FASTA

>9KB7_2 R-spondin-2 (chains B)
MQFRLFSFALIILNCMDYSHCQGNRWRRSKRASYVSNPICKGCLSCSKDNGCSRCQQKLF
FFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLH
RGRCFDECPDGFAPLEETMECVEENLYFQGHHHHHHHHHH

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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