8Y69: LGR4-RSPO2-ZNRF3

LGR4-RSPO2-ZNRF3 (2:2:2). Determined by electron microscopy at 3.38 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.38 Å
Organisms: Homo sapiens, Camelus bactrianus
Chains: 8
Atoms: 17,577
Mol. weight: 359.49 kDa
Ligands: CLR
Released: 4 Dec 2024

Explore 8Y69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y69 contains 59 α-helices and 130 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: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	40-42	3	1
β-strand	61-64	4	1
β-strand	72	1	2
α-helix	73	1
β-strand	85-88	4	1
β-strand	96	1	2
β-strand	109-111	3	1
α-helix	122-125	4
β-strand	133-135	3	1
β-strand	157-162	6	1
α-helix	170-174	5
β-strand	181-186	6	1
β-strand	191-192	2	3
α-helix	193	1
β-strand	205-207	3	1
β-strand	215-216	2	3
β-strand	229-231	3	1
α-helix	242-246	5
β-strand	252-254	3	1
β-strand	262	1	4
α-helix	263-264	2
β-strand	276-278	3	1
β-strand	286	1	4
β-strand	300-303	4	5
α-helix	312-314	3
β-strand	323-326	4	5
β-strand	347-349	3	5
β-strand	369-371	3	5
β-strand	379-380	2	6
α-helix	382-385	4
β-strand	393-395	3	5
β-strand	403-404	2	6
β-strand	417-419	3	5
β-strand	438-440	3	5
α-helix	449-452	4
β-strand	461-463	3	5
α-helix	467-472	6
β-strand	521-522	2	5
α-helix	539-554	16
α-helix	556-563	8
α-helix	572-600	29
α-helix	605-613	9
α-helix	617-648	32
α-helix	662-682	21
α-helix	704-731	28
α-helix	740-742	3
α-helix	743-759	17
α-helix	761-767	7
α-helix	779-789	11
α-helix	797-804	8
α-helix	806-817	12

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-66	9	7
β-strand	76-85	10	7
β-strand	89	1	8
β-strand	94-101	8	7
β-strand	120-125	6	7
α-helix	139-148	10
β-strand	153-157	5	7
α-helix	164-169	6
β-strand	176	1	8
β-strand	180-182	3	7
α-helix	187-197	11
β-strand	202-205	4	7
α-helix	219-232	14
α-helix	234-242	9

Chain D: 20 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	17
β-strand	40-42	3	17
β-strand	61-63	3	17
β-strand	71-72	2	18
α-helix	73	1
β-strand	85-87	3	17
β-strand	95-96	2	18
β-strand	109-111	3	17
β-strand	114	1	19
β-strand	119	1	20
β-strand	133-135	3	17
β-strand	138	1	19
β-strand	143	1	20
β-strand	159	1	17
α-helix	170-173	4
β-strand	181-183	3	17
β-strand	191-192	2	21
β-strand	205-207	3	17
β-strand	215-216	2	21
β-strand	229-231	3	17
α-helix	242-246	5
β-strand	252-254	3	17
β-strand	262	1	22
α-helix	263-264	2
β-strand	276-278	3	17
β-strand	286	1	22
β-strand	301-303	3	23
α-helix	312-314	3
β-strand	324-326	3	23
β-strand	328	1	24
β-strand	348-349	2	23
β-strand	352	1	24
α-helix	358-360	3
β-strand	369-371	3	23
β-strand	380	1	25
β-strand	393-395	3	23
β-strand	404	1	25
β-strand	417-419	3	23
β-strand	438-440	3	23
β-strand	461-463	3	23
α-helix	467-470	4
α-helix	471-473	3
β-strand	521-522	2	23
α-helix	539-551	13
α-helix	554-563	10
α-helix	572-600	29
α-helix	606-614	9
α-helix	618-647	30
α-helix	659-682	24
α-helix	704-726	23
α-helix	728-731	4
α-helix	744-765	22
α-helix	779-789	11
α-helix	796-803	8
α-helix	808-819	12

Chain E: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	9
β-strand	444-448	5	9
β-strand	457-464	8	10
β-strand	466	1	11
β-strand	468	1	11
β-strand	470-476	7	10
β-strand	482-484	3	10
β-strand	489	1	12
β-strand	492	1	12
β-strand	493-497	5	9
β-strand	502-506	5	9
α-helix	512-514	3
β-strand	516-523	8	10
α-helix	534-536	3
β-strand	539-540	2	10
β-strand	544-546	3	10

Chain G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	13
β-strand	51	1	13
β-strand	60-65	6	13
β-strand	70-75	6	13
β-strand	82-85	4	13
β-strand	91-95	5	13
α-helix	96	1
β-strand	101-104	4	14
β-strand	110-113	4	14
β-strand	118	1	15
β-strand	119	1	16
β-strand	125	1	15
β-strand	140	1	16

Chain H: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-65	8	26
β-strand	77-85	9	26
β-strand	89	1	27
β-strand	94-100	7	26
α-helix	103-105	3
α-helix	116-117	2
β-strand	120-125	6	26
α-helix	126-128	3
α-helix	139-149	11
β-strand	153-157	5	26
α-helix	164-170	7
β-strand	176	1	27
β-strand	180-182	3	26
α-helix	187-197	11
β-strand	202-206	5	26
α-helix	217-242	26

Chain I: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	28
β-strand	443-446	4	29
β-strand	447-449	3	28
β-strand	457-464	8	30
β-strand	466	1	31
β-strand	468	1	31
β-strand	470-476	7	30
β-strand	482-484	3	30
β-strand	492-497	6	29
β-strand	502-507	6	29
β-strand	516-523	8	30
β-strand	539-540	2	30
β-strand	544-546	3	30

Chain J: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	32
β-strand	51	1	32
β-strand	60-65	6	32
β-strand	70-75	6	32
β-strand	82-85	4	32
β-strand	92-95	4	32
α-helix	96	1
β-strand	101-106	6	33
β-strand	109-113	5	33
β-strand	118	1	34
β-strand	125	1	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A, D	protein	788	Homo sapiens	Q9BXB1 (AlphaFold model)
E3 ubiquitin-protein ligase ZNRF3	C, H	protein	188	Homo sapiens	Q9ULT6 (AlphaFold model)
MB52	E, I	protein	560	Camelus bactrianus
R-spondin-2	G, J	protein	101	Homo sapiens	Q6UXX9 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8Y69_1 Leucine-rich repeat-containing G-protein coupled receptor 4 (chains A, D)
CSCDGDRRVDCSGKGLTAVPEGLSAFTQALDISMNNITQLPEDAFANFPFLEELQLAGND
LSFIHPKALSGLKELKVLTLQNNQLKTVPSEAIRGLSALQSLRLDANHITSVPEDSFEGL
VQLRHLWLDDNSLTEVPVHPLSNLPTLQALTLALNKISSIPDFAFTNLSSLVVLHLHNNK
IRSLSQHCFDGLDNLETLDLNYNNLGEFPQAIKALPSLKELGFHSNSISVIPDGAFDGNP
LLRTIHLYDNPLSFVGNSAFHNLSDLHSLVIRGASMVQQFPNLTGTVHLESLTLTGTKIS
SIPNNLCQEQKMLRTLDLSYNNIRDLPSFNGCHALEEISLQRNQIYQIKEGTFQGLISLR
ILDLSRNLIHEIHSRAFATLGPITNLDVSFNELTSFPTEGLNGLNQLKLVGNFKLKEALA
AKDFVNLRSLSVPYAYQCCAFWGCDSYANLNTEDNSLQDHSVAQEKGTADAANVTSTLEN
EEHSQIIIHCTPSTGAFKPCEYLLGSWMIRLTVWFIFLVALFFNLLVILTTFACATSLPS
SKLFIGLISVSNLFMGIYTGILTFLDAVSWGRFAEFGIWWETGSGCKVAGFLAVFSSESA
IFLLMLATVERSLSAKDIMKNGKSNHLKQFRVAALLAFLGATVAGCFPLFHRGEYSASPL
CLPFPTGETPSLGFTVTLVLLNSLAFLLMAVIYTKLYCNLEKEDLSENSQSSMIKHVAWL
IFTNCIFFCPVAFFSFAPLITAISISPEIMKSVTLIFFPLPACLNPVLYVFFNPKFKEDW
KLLKRRVT

Sequence of entity 2 (C, H), FASTA

>8Y69_2 E3 ubiquitin-protein ligase ZNRF3 (chains C, H)
KETAFVEVVLFESSPSGDYTTYTTGLTGRFSRAGATLSAEGEIVQMHPLGLCNNNDEEDL
YEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDP
LKRPVVYVKGADAIKLMNIVNKQKVARARIQHRPPRQPTEYFDMGIFLAFFVVVSLVCLI
LLVKIKLK

Sequence of entity 3 (E, I), FASTA

>8Y69_3 MB52 (chains E, I)
MKKIWLALAGLVLAFSASAQVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTL
KDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQET
QQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGH
LKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQN
LANTLIQELGNNPFRASGGGSGGGGSGKLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVN
NLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYT
DENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAG
LAPLNSKGEKLEAHVTTSKYGSLRLSCAASGYTYSPYCMGWFRQAPGKAREGVATVDLDG
STIYADSVKGRFTISQDNAKNTLYLQMNSLKPEDTAMYYCASRTRAGVTCGLNWAIFSYW
GQGTQVTVSSHHHHHHEPEA

Sequence of entity 4 (G, J), FASTA

>8Y69_4 R-spondin-2 (chains G, J)
KGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIEN
CDSCFSKDFCTKCKVGFYLHRGRCFDECPAGFAPLDETMEC

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2

Primary citation

Structural insights into the LGR4-RSPO2-ZNRF3 complexes regulating WNT/ beta-catenin signaling. Wang, L., Hu, F., Cui, Q. et al. Nat Commun (2025) 16:362-362. DOI 10.1038/s41467-024-55431-3 · 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

Browse structure collections

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