9KB8: LGR4-RSPO2-ZNRF3 complex

Cryo-EM structure of LGR4-RSPO2-ZNRF3 complex (1:1:2). Determined by electron microscopy at 3.25 Å resolution. Released 15 Oct 2025.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,396
Mol. weight: 164.99 kDa
Ligands: NAG
Released: 15 Oct 2025

Explore 9KB8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KB8 contains 35 α-helices and 66 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: 19 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	3
β-strand	40-42	3	3
β-strand	61-63	3	3
β-strand	71-72	2	4
β-strand	85-87	3	3
β-strand	95-96	2	4
β-strand	109-111	3	3
β-strand	119	1	5
α-helix	124-127	4
β-strand	133-135	3	3
β-strand	143	1	5
β-strand	157-159	3	3
α-helix	170-173	4
β-strand	181-183	3	3
β-strand	191-192	2	6
β-strand	205-207	3	3
β-strand	215-216	2	6
β-strand	229-231	3	3
α-helix	242-246	5
β-strand	252-254	3	3
β-strand	262-263	2	7
β-strand	276-278	3	3
β-strand	286-287	2	7
β-strand	300-304	5	8
β-strand	323-327	5	8
β-strand	333	1	9
α-helix	338-341	4
β-strand	347-349	3	8
β-strand	357	1	9
β-strand	369-371	3	8
β-strand	380	1	10
β-strand	393-395	3	8
β-strand	404	1	10
β-strand	417-419	3	8
β-strand	438-440	3	8
α-helix	450-452	3
α-helix	453-455	3
β-strand	461-463	3	8
α-helix	467-470	4
β-strand	521-523	3	8
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	701-731	31
α-helix	734-737	4
α-helix	742-768	27
α-helix	769-771	3
α-helix	779-789	11
α-helix	792-804	13
α-helix	806-821	16

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-68	11	1
β-strand	74-85	12	1
β-strand	89	1	2
β-strand	94-101	8	1
α-helix	103-106	4
α-helix	111-113	3
α-helix	116-117	2
β-strand	120-125	6	1
α-helix	129-131	3
α-helix	139-148	10
β-strand	151-157	7	1
α-helix	163-169	7
β-strand	176	1	2
β-strand	180-183	4	1
α-helix	186-197	12
β-strand	201-206	6	1
α-helix	215-246	32

Chain C: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	11
β-strand	51-55	5	11
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	101-106	6	12
β-strand	109-113	5	12
β-strand	118-120	3	13
β-strand	123-125	3	13
β-strand	133-135	3	14
β-strand	140-142	3	14

Chain D: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	58-65	8	15
β-strand	68	1	16
β-strand	74	1	16
β-strand	77-80	4	15
β-strand	83-85	3	15
β-strand	89	1	17
β-strand	94-100	7	15
α-helix	103-106	4
α-helix	111-114	4
α-helix	116-117	2
β-strand	120-125	6	15
α-helix	126-128	3
α-helix	129-131	3
α-helix	139-148	10
β-strand	153-157	5	15
α-helix	164-169	6
β-strand	176	1	17
β-strand	180-183	4	15
α-helix	186-197	12
β-strand	202-206	5	15

Molecules and chains

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

Sequence of entity 1 (B, D), FASTA

>9KB8_1 E3 ubiquitin-protein ligase ZNRF3 (chains B, D)
METGLRWLLLVAVLKGVQCKETAFVEVVLFESSPSGDYTTYTTGLTGRFSRAGATLSAEG
EIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIF
DVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHRPPRQPTEY
FDMGIFLAFFVVVSLVCLILLVKIKLKQRRSQNSMNRLAVQALEKMETRKF

Sequence of entity 2 (A), FASTA

>9KB8_2 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 3 (C), FASTA

>9KB8_3 R-spondin-2 (chains C)
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 Q9ULT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8G4Y 1.41 Å, Structure of ZNRF3 ECD bound to peptide MK1-3.6.10
9OZX 2.4 Å, Crystal structure of ZNRF3 RING in complex with UbcH5b
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)
8Y69 3.38 Å, LGR4-RSPO2-ZNRF3 (2:2:2)
9KB9 3.59 Å, Cryo-EM structure of LGR4-RSPO2-ZNRF3 complex (2:2:2)
4UFS 4.8 Å, Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5…

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