8WVX: LGR4

Cryo-EM structure of LGR4 in complex with Norrin(dimer). Determined by electron microscopy at 3.32 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 3.32 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,460
Mol. weight: 207.33 kDa
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

8WVX contains 42 α-helices and 70 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: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	40-41	2	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
α-helix	123-126	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
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	301-304	4	5
α-helix	312-314	3
β-strand	323-327	5	5
α-helix	338-341	4
β-strand	347-349	3	5
β-strand	369-371	3	5
β-strand	379-380	2	6
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	450-452	3
β-strand	461-463	3	5
α-helix	467-473	7
α-helix	539-565	27
α-helix	574-600	27
α-helix	610-613	4
α-helix	616-646	31
α-helix	659-678	20
α-helix	679-681	3
α-helix	706-730	25
α-helix	741-767	27
α-helix	769-772	4
α-helix	773-775	3
α-helix	781-789	9
α-helix	793-799	7
α-helix	800-804	5
α-helix	808-819	12

Chain B: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	41-42	2	7
β-strand	61-63	3	7
β-strand	72	1	8
β-strand	85-87	3	7
β-strand	96	1	8
β-strand	109-111	3	7
β-strand	133-135	3	7
β-strand	157-159	3	7
α-helix	170-173	4
β-strand	181-183	3	7
β-strand	191-192	2	9
β-strand	205-207	3	7
β-strand	215-216	2	9
β-strand	229-231	3	7
β-strand	252-254	3	7
β-strand	262-263	2	10
β-strand	276-278	3	7
β-strand	286-287	2	10
β-strand	301-304	4	11
α-helix	312-314	3
β-strand	323-327	5	11
α-helix	338-341	4
β-strand	347-349	3	11
β-strand	369-371	3	11
β-strand	379-380	2	12
β-strand	393-395	3	11
β-strand	403-404	2	12
β-strand	417-419	3	11
β-strand	438-440	3	11
α-helix	450-452	3
β-strand	461-463	3	11
α-helix	467-469	3
α-helix	470-473	4
α-helix	539-563	25
α-helix	572-600	29
α-helix	610-613	4
α-helix	616-646	31
α-helix	659-678	20
α-helix	707-730	24
α-helix	741-767	27
α-helix	769-772	4
α-helix	773-775	3
α-helix	779-789	11
α-helix	792-795	4
α-helix	797-799	3
α-helix	800-804	5
α-helix	806-819	14

Chain C: 0 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	40-48	9	13
β-strand	58-67	10	13
β-strand	73-77	5	14
β-strand	80	1	15
β-strand	89-92	4	14
β-strand	94-106	13	16
β-strand	118-130	13	16

Chain D: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	38	1	17
β-strand	40-48	9	14
α-helix	55-57	3
β-strand	58-67	10	14
β-strand	68	1	17
α-helix	72	1
β-strand	73-77	5	13
β-strand	80	1	16
β-strand	89-92	4	13
β-strand	94-107	14	15
β-strand	117-130	14	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A, B	protein	832	Homo sapiens	Q9BXB1 (AlphaFold model)
Norrin	C, D	protein	103	Homo sapiens	Q00604 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8WVX_1 Leucine-rich repeat-containing G-protein coupled receptor 4 (chains A, B)
MKTIIALSYIFCLVFADYKDDDDAAPPLCAAPCSCDGDRRVDCSGKGLTAVPEGLSAFTQ
ALDISMNNITQLPEDAFKNFPFLEELQLAGNDLSFIHPKALSGLKELKVLTLQNNQLKTV
PSEAIRGLSALQSLRLDANHITSVPEDSFEGLVQLRHLWLDDNSLTEVPVHPLSNLPTLQ
ALTLALNKISSIPDFAFTNLSSLVVLHLHNNKIRSLSQHCFDGLDNLETLDLNYNNLGEF
PQAIKALPSLKELGFHSNSISVIPDGAFDGNPLLRTIHLYDNPLSFVGNSAFHNLSDLHS
LVIRGASMVQQFPNLTGTVHLESLTLTGTKISSIPNNLCQEQKMLRTLDLSYNNIRDLPS
FNGCHALEEISLQRNQIYQIKEGTFQGLISLRILDLSRNLIHEIHSRAFATLGPITNLDV
SFNELTSFPTEGLNGLNQLKLVGNFKLKEALAAKDFVNLRSLSVPYAYQCCAFWGCDSYA
NLNTEDNSLQDHSVAQEKGTADAANVTSTLENEEHSQIIIHCTPSTGAFKPCEYLLGSWM
IRLTVWFIFLVALFFNLLVILTTFASCTSLPSSKLFIGLISVSNLFMGIYTGILTFLDAV
SWGRFAEFGIWWETGSGCKVAGFLAVFSSESAIFLLMLATVERSLSAKDIMKNGKSNHLK
QFRVAALLAFLGATVAGCFPLFHRGEYSASPLCLPFPTGETPSLGFTVTLVLLNSLAFLL
MAVIYTKLYCNLEKEDLSENSQSSMIKHVAWLIFTNCIFFCPVAFFSFAPLITAISISPE
IMKSVTLIFFPLPACLNPVLYVFFNPKFKEDWKLLKRRVTKKSGSVSVSISS

Sequence of entity 2 (C, D), FASTA

>8WVX_2 Norrin (chains C, D)
IMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFR
SSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS

Primary citation

Cryo-EM structure of LGR4 in complex with Norrin (dimer). 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

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