8XFP: PDB entry 8XFP

the pentamerA complex of LGR4-RSPO2-ZNRF3(delta RING). Determined by electron microscopy at 3.21 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Homo sapiens, Camelus bactrianus
Chains: 6
Atoms: 10,742
Mol. weight: 388.93 kDa
Released: 4 Dec 2024

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

Secondary structure: helices and β-sheets

8XFP contains 33 α-helices and 85 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: 17 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	72	1	2
β-strand	85-87	3	1
β-strand	96	1	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	243-246	4
β-strand	252-254	3	1
β-strand	262	1	5
β-strand	276-278	3	1
β-strand	286	1	5
β-strand	300-303	4	6
β-strand	323-326	4	6
α-helix	336-338	3
β-strand	347-349	3	6
β-strand	369-371	3	6
β-strand	379-380	2	7
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	450-451	2
β-strand	461-463	3	6
α-helix	469-471	3
β-strand	521-522	2	6
α-helix	539-566	28
α-helix	572-600	29
α-helix	605-614	10
α-helix	616-648	33
α-helix	659-682	24
α-helix	687-689	3
α-helix	695-698	4
α-helix	704-731	28
α-helix	743-768	26
α-helix	779-789	11
α-helix	792-803	12
α-helix	806-819	14

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-66	9	10
β-strand	76-85	10	10
β-strand	89	1	11
β-strand	94-100	7	10
α-helix	103-105	3
β-strand	120-125	6	10
α-helix	139-148	10
β-strand	151-157	7	10
α-helix	163-170	8
α-helix	171-173	3
β-strand	176	1	11
β-strand	180-183	4	10
α-helix	186-197	12
β-strand	202-206	5	10
α-helix	214-219	6
α-helix	222-226	5
α-helix	228-238	11

Chain E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	8
β-strand	444-449	6	8
β-strand	457-464	8	9
β-strand	470-476	7	9
β-strand	482-484	3	9
β-strand	489	1	8
β-strand	492-497	6	8
β-strand	502-507	6	8
α-helix	512-514	3
β-strand	516-523	8	9
β-strand	539-540	2	9
β-strand	544-546	3	9

Chain G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	12
β-strand	47	1	13
β-strand	51	1	13
β-strand	55	1	12
β-strand	60-66	7	13
β-strand	69-75	7	13
β-strand	82-85	4	13
β-strand	92-95	4	13
α-helix	96	1
β-strand	101-103	3	14
β-strand	112-113	2	14
β-strand	118-119	2	15
β-strand	124-125	2	15

Chain H: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	58-66	9	16
β-strand	76-85	10	16
β-strand	89	1	17
β-strand	94-101	8	16
α-helix	103-105	3
β-strand	121-125	5	16
α-helix	129-131	3
α-helix	139-148	10
β-strand	154-157	4	16
α-helix	163-170	8
α-helix	171-173	3
β-strand	176	1	17
β-strand	180-183	4	16
α-helix	186-197	12
β-strand	202-206	5	16

Chain J: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	18
β-strand	47	1	19
β-strand	51	1	19
β-strand	55	1	18
β-strand	60-66	7	19
β-strand	69-75	7	19
β-strand	82-85	4	19
β-strand	91-95	5	19
β-strand	101-106	6	20
β-strand	109-113	5	20
β-strand	118-119	2	21
β-strand	124-125	2	21
β-strand	140	1	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A	protein	951	Homo sapiens	Q9BXB1 (AlphaFold model)
nanobody Nb52	E	protein	560	Camelus bactrianus
E3 ubiquitin-protein ligase ZNRF3	C, H	protein	936	Homo sapiens	Q9ULT6 (AlphaFold model)
R-spondin-2	G, J	protein	101	Homo sapiens	Q6UXX9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8XFP_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
IMKSVTLIFFPLPACLNPVLYVFFNPKFKEDWKLLKRRVTKKSGSVSVSISSQGGCLEQD
FYYDCGMYSHLQGNLTVCDCCESFLLTKPVSCKHLIKSHSCPALAVASCQRPEGYWSDCG
TQSAHSDYADEEDSFVSDSSDQVQACGRACFYQSRGFPLVRYAYNLPRVKD

Sequence of entity 2 (E), FASTA

>8XFP_2 nanobody Nb52 (chains E)
MKKIWLALAGLVLAFSASAQVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTL
KDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQET
QQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGH
LKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQN
LANTLIQELGNNPFRASGGGSGGGGSGKLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVN
NLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYT
DENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAG
LAPLNSKGEKLEAHVTTSKYGSLRLSCAASGYTYSPYCMGWFRQAPGKAREGVATVDLDG
STIYADSVKGRFTISQDNAKNTLYLQMNSLKPEDTAMYYCASRTRAGVTCGLNWAIFSYW
GQGTQVTVSSHHHHHHEPEA

Sequence of entity 3 (C, H), FASTA

>8XFP_3 E3 ubiquitin-protein ligase ZNRF3 (chains C, H)
MRPRSGGRPGATGRRRRRLRRRPRGLRCSRLPPPPPLPLLLGLLLAAAGPGAARAKETAF
VEVVLFESSPSGDYTTYTTGLTGRFSRAGATLSAEGEIVQMHPLGLCNNNDEEDLYEYGW
VGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPV
VYVKGADAIKLMNIVNKQKVARARIQHRPPRQPTEYFDMGIFLAFFVVVSLVCLILLVKI
KLKQRRSQNSMNRLAVQALEKMETRKFNSKSKGRREGSCGALDTLSSSSTSDCAICLEKY
IDGEELRVIPCTHRFHRKCVDPWLLQHHTCPHCRHNIIEQKGNPSAVCVETSNLSRGRQQ
RVTLPVHYPGRVHRTNAIPAYPTRTSMDSHGNPVTLLTMDRHGEQSLYSPQTPAYIRSYP
PLHLDHSLAAHRCGLEHRAYSPAHPFRRPKLSGRSFSKAACFSQYETMYQHYYFQGLSYP
EQEGQSPPSLAPRGPARAFPPSGSGSLLFPTVVHVAPPSHLESGSTSSFSCYHGHRSVCS
GYLADCPGSDSSSSSSSGQCHCSSSDSVVDCTEVSNQGVYGSCSTFRSSLSSDYDPFIYR
SRSPCRASEAGGSGSSGRGPALCFEGSPPPEELPAVHSHGAGRGEPWPGPASPSGDQVST
CSLEMNYSSNSSLEHRGPNSSTSEVGLEASPGAAPDLRRTWKGGHELPSCACCCEPQPSP
AGPSAGAAGSSTLFLGPHLYEGSGPAGGEPQSGSSQGLYGLHPDHLPRTDGVKYEGLPCC
FYEEKQVARGGGGGSGCYTEDYSVSVQYTLTEEPPPGCYPGARDLSQRIPIIPEDVDCDL
GLPSDCQGTHSLGSWGGTRGPDTPRPHRGLGATREEERALCCQARALLRPGCPPEEAGAV
RANFPSALQDTQESSTTATEAAGPRSHSADSSSPGA

Sequence of entity 4 (G, J), FASTA

>8XFP_4 R-spondin-2 (chains G, J)
KGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIEN
CDSCFSKDFCTKCKVGFYLHRGRCFDECPAGFAPLDETMEC

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)
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
8WVX 3.32 Å, Cryo-EM structure of LGR4 in complex with Norrin(dimer)

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