8WVU: LGR4

Cryo-EM structure of LGR4 in complex with Rspo1 and RNF43. Determined by electron microscopy at 3.61 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 3.61 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,427
Mol. weight: 123.68 kDa
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

8WVU contains 23 α-helices and 50 β-strands across 3 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	1
β-strand	40-42	3	1
α-helix	51-52	2
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
α-helix	124-127	4
β-strand	133-135	3	1
β-strand	157-159	3	1
α-helix	170-173	4
β-strand	181-183	3	1
β-strand	191-192	2	3
β-strand	205-207	3	1
β-strand	215-216	2	3
β-strand	229-231	3	1
α-helix	243-246	4
β-strand	252-254	3	1
β-strand	262-263	2	4
β-strand	276-278	3	1
β-strand	286-287	2	4
β-strand	302-303	2	5
β-strand	323-326	4	5
α-helix	338-341	4
β-strand	347-349	3	5
β-strand	369-371	3	5
β-strand	380	1	6
β-strand	393-395	3	5
β-strand	404	1	6
β-strand	417-419	3	5
β-strand	438-440	3	5
β-strand	462-463	2	5
α-helix	467-471	5
α-helix	517-521	5
α-helix	539-563	25
α-helix	576-600	25
α-helix	609-613	5
α-helix	618-645	28
α-helix	662-682	21
α-helix	704-730	27
α-helix	742-758	17
α-helix	761-767	7
α-helix	769-772	4
α-helix	779-789	11
α-helix	792-803	12
α-helix	806-817	12

Chain B: 0 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	44-46	3	7
β-strand	52	1	8
β-strand	55-56	2	7
β-strand	61	1	9
β-strand	64-66	3	8
β-strand	71-73	3	8
β-strand	76	1	9
β-strand	83-84	2	10
β-strand	95-96	2	10
β-strand	102-104	3	11
β-strand	107	1	12
β-strand	110	1	12
β-strand	113-114	2	11
β-strand	119-121	3	13
β-strand	124-126	3	13
β-strand	141	1	13

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	49	1	14
β-strand	81-84	4	15
α-helix	87-89	3
β-strand	103-108	6	15
α-helix	122-131	10
β-strand	134-140	7	15
α-helix	145-149	5
β-strand	161-163	3	15
α-helix	169-177	9
β-strand	187	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A	protein	832	Homo sapiens	Q9BXB1 (AlphaFold model)
R-spondin-1	B	protein	121	Homo sapiens	Q2MKA7 (AlphaFold model)
E3 ubiquitin-protein ligase RNF43	C	protein	166	Homo sapiens	Q68DV7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8WVU_1 Leucine-rich repeat-containing G-protein coupled receptor 4 (chains A)
MKTIIALSYIFCLVFADYKDDDDAAPPLCAAPCSCDGDRRVDCSGKGLTAVPEGLSAFTQ
ALDISMNNITQLPEDAFKNFPFLEELQLAGNDLSFIHPKALSGLKELKVLTLQNNQLKTV
PSEAIRGLSALQSLRLDANHITSVPEDSFEGLVQLRHLWLDDNSLTEVPVHPLSNLPTLQ
ALTLALNKISSIPDFAFTNLSSLVVLHLHNNKIRSLSQHCFDGLDNLETLDLNYNNLGEF
PQAIKALPSLKELGFHSNSISVIPDGAFDGNPLLRTIHLYDNPLSFVGNSAFHNLSDLHS
LVIRGASMVQQFPNLTGTVHLESLTLTGTKISSIPNNLCQEQKMLRTLDLSYNNIRDLPS
FNGCHALEEISLQRNQIYQIKEGTFQGLISLRILDLSRNLIHEIHSRAFATLGPITNLDV
SFNELTSFPTEGLNGLNQLKLVGNFKLKEALAAKDFVNLRSLSVPYAYQCCAFWGCDSYA
NLNTEDNSLQDHSVAQEKGTADAANVTSTLENEEHSQIIIHCTPSTGAFKPCEYLLGSWM
IRLTVWFIFLVALFFNLLVILTTFASCTSLPSSKLFIGLISVSNLFMGIYTGILTFLDAV
SWGRFAEFGIWWETGSGCKVAGFLAVFSSESAIFLLMLATVERSLSAKDIMKNGKSNHLK
QFRVAALLAFLGATVAGCFPLFHRGEYSASPLCLPFPTGETPSLGFTVTLVLLNSLAFLL
MAVIYTKLYCNLEKEDLSENSQSSMIKHVAWLIFTNCIFFCPVAFFSFAPLITAISISPE
IMKSVTLIFFPLPACLNPVLYVFFNPKFKEDWKLLKRRVTKKSGSVSVSISS

Sequence of entity 2 (B), FASTA

>8WVU_2 R-spondin-1 (chains B)
EGSQACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMNKC
IKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGSSAANGTMECSSAAAHHHHHHH
H

Sequence of entity 3 (C), FASTA

>8WVU_3 E3 ubiquitin-protein ligase RNF43 (chains C)
QKAIIRVIPLKMDPTGKLNLTLEGVFAGVAEITPAEGKLMQSHPLYLCNASDDDNLEPGF
ISIVKLESPRRAPRPCLSLASKARMAGERGASAVLFDITEDRAAAEQLQQPLGLTWPVVL
IWGNDAEKLMEFVYKNQKAHVRIELKEPPAWPDYDAAAHHHHHHHH

Primary citation

Cryo-EM structure of LGR4 in complex with Rspo1 and RNF43. Lin, C., Chang, Z. To be published.

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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