4KNG: Human LGR5-RSPO1-RNF43

Crystal structure of human LGR5-RSPO1-RNF43. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,252
Mol. weight: 178.88 kDa
Ligands: NAG, NI
Released: 19 Jun 2013

Explore 4KNG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KNG contains 18 α-helices and 100 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: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	39-43	5	1
β-strand	47-51	5	1
β-strand	68-72	5	1
β-strand	94-96	3	1
β-strand	118-120	3	1
β-strand	128	1	2
β-strand	142-144	3	1
β-strand	152	1	2
β-strand	166-168	3	1
α-helix	179-182	4
β-strand	190-192	3	1
β-strand	200-201	2	3
β-strand	214-216	3	1
β-strand	224-225	2	3
β-strand	238-240	3	1
α-helix	251-255	5
β-strand	261-263	3	1
β-strand	271-272	2	4
β-strand	285-287	3	1
β-strand	295-296	2	4
β-strand	310-313	4	5
α-helix	321-323	3
β-strand	332-336	5	5
α-helix	347-350	4
β-strand	356-358	3	5
β-strand	378-380	3	5
β-strand	388-389	2	6
β-strand	402-404	3	5
β-strand	412-413	2	6
β-strand	426-428	3	5
β-strand	447-449	3	5
β-strand	470-472	3	5
β-strand	540	1	5

Chain B: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	39-43	5	7
β-strand	47-51	5	7
β-strand	68-72	5	7
β-strand	94-96	3	7
β-strand	118-120	3	7
β-strand	128	1	8
β-strand	142-144	3	7
β-strand	152	1	8
β-strand	166-168	3	7
α-helix	179-182	4
β-strand	190-192	3	7
β-strand	200-201	2	9
β-strand	214-216	3	7
β-strand	224-225	2	9
β-strand	238-240	3	7
α-helix	251-255	5
β-strand	261-263	3	7
β-strand	271-272	2	10
β-strand	285-287	3	7
β-strand	295-296	2	10
β-strand	310-313	4	11
α-helix	321-323	3
β-strand	332-336	5	11
α-helix	347-350	4
β-strand	356-358	3	11
β-strand	378-380	3	11
β-strand	388-389	2	12
β-strand	402-404	3	11
β-strand	412-413	2	12
β-strand	426-428	3	11
β-strand	435	1	13
β-strand	447-449	3	11
β-strand	455	1	13
β-strand	470-472	3	11
α-helix	477-480	4
β-strand	540	1	11

Chain E: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	45-52	8	22
β-strand	63-69	7	22
β-strand	73	1	23
β-strand	78-84	7	22
α-helix	99-100	2
β-strand	104-108	5	22
α-helix	122-131	10
β-strand	136-140	5	22
α-helix	142-144	3
α-helix	147-150	4
β-strand	157	1	23
β-strand	161-164	4	22
α-helix	166-176	11
β-strand	184-189	6	22

Chain F: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	45-52	8	24
β-strand	63-69	7	24
β-strand	73	1	25
β-strand	78-84	7	24
β-strand	104-108	5	24
α-helix	122-132	11
β-strand	137-140	4	24
α-helix	142-144	3
α-helix	147-150	4
β-strand	157	1	25
β-strand	161-164	4	24
α-helix	166-174	9
β-strand	184-189	6	24

Chains M and P: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	44-46	3	14
β-strand	52	1	15
β-strand	55-56	2	14
β-strand	61-66	6	15
β-strand	71-76	6	15
β-strand	83-86	4	15
β-strand	93-96	4	15
β-strand	102-107	6	16
β-strand	110-114	5	16
β-strand	119-121	3	17
β-strand	124-126	3	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 5	A, B	protein	531	Homo sapiens	O75473 (AlphaFold model)
R-spondin-1	M, P	protein	115	Homo sapiens	Q2MKA7 (AlphaFold model)
E3 ubiquitin-protein ligase RNF43	E, F	protein	160	Homo sapiens	Q68DV7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KNG_1 Leucine-rich repeat-containing G-protein coupled receptor 5 (chains A, B)
GPRGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVFTSYLDLSMNNISQLLPNPLPSL
RFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLRHVPTEALQNLRSLQSLRLDANH
ISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSALQAMTLALNKIHHIPDYAFGNL
SSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLDEFPTAIRTLSNLKELGFHSNNI
RSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPELRTLTLNGASQITEFPDLTGTAN
LESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDLPSFSVCQKLQKIDLRHNEIYEI
KVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKLDLSSNLLSSFPITGLHGLTHLK
LTGNHALQSLISSENFPELKVIEMPYAYQCCAFGVCENAYKISNQWNKGDNSSMDDLHKK
DAGMFQAQDERDLEDFLLDFEEDLKALHSVQCSPSPGPFKPCEHLLDGAAA

Sequence of entity 2 (M, P), FASTA

>4KNG_2 R-spondin-1 (chains M, P)
GPEGSQACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMN
KCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGSSAANGTMECSSAAA

Sequence of entity 3 (E, F), FASTA

>4KNG_3 E3 ubiquitin-protein ligase RNF43 (chains E, F)
GPQKAIIRVIPLKMDPTGKLNLTLEGVFAGVAEITPAEGKLMQSHPLYLCNASDDDNLEP
GFISIVKLESPRRAPRPCLSLASKARMAGERGASAVLFDITEDRAAAEQLQQPLGLTWPV
VLIWGNDAEKLMEFVYKNQKAHVRIELKEPPAWPDYDAAA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
NI	Nickel (II) ion	Ni	1

Primary citation

The structural basis of R-spondin recognition by LGR5 and RNF43. Chen, P.H., Chen, X., Lin, Z. et al. Genes Dev (2013) 27:1345-1350. DOI 10.1101/gad.219915.113 · PubMed

Other PDB entries of the same protein (UniProt O75473 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UFR 2.2 Å, Structure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2)
4BSR 3.2 Å, Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121…
4BSS 3.2 Å, Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal…
4BSU 3.2 Å, Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in C2 crystal…
4BST 4.3 Å, Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P6122…
4UFS 4.8 Å, Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5…

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