4BSS: Ectodomain of LGR5

Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form. Determined by X-ray diffraction at 3.2 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 17,925
Mol. weight: 298.88 kDa
Ligands: NAG
Released: 19 Jun 2013

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

Secondary structure: helices and β-sheets

4BSS contains 26 α-helices and 151 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: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-42	4	1
β-strand	48-51	4	1
β-strand	68-72	5	1
β-strand	94-96	3	1
β-strand	118-120	3	1
β-strand	142-144	3	1
β-strand	166-168	3	1
α-helix	179-182	4
β-strand	190-192	3	1
β-strand	200-201	2	2
β-strand	214-216	3	1
β-strand	224-225	2	2
β-strand	238-240	3	1
α-helix	251-255	5
β-strand	261-263	3	1
β-strand	271-272	2	3
β-strand	285-287	3	1
β-strand	295-296	2	3
β-strand	309-313	5	4
α-helix	321-323	3
β-strand	332-336	5	4
α-helix	347-349	3
β-strand	356-358	3	4
β-strand	378-380	3	4
β-strand	388-389	2	5
β-strand	402-404	3	4
β-strand	412-413	2	5
β-strand	426-428	3	4
β-strand	447-449	3	4
β-strand	470-472	3	4
α-helix	476-480	5

Chain B: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	6
β-strand	48-51	4	6
β-strand	68-72	5	6
β-strand	94-96	3	6
β-strand	118-120	3	6
β-strand	128	1	7
β-strand	142-144	3	6
β-strand	152	1	7
β-strand	166-168	3	6
α-helix	179-183	5
β-strand	190-192	3	6
β-strand	200-201	2	8
β-strand	214-216	3	6
β-strand	224-225	2	8
β-strand	238-240	3	6
α-helix	251-255	5
β-strand	261-263	3	6
β-strand	271-272	2	9
β-strand	285-287	3	6
β-strand	295-296	2	9
β-strand	309-313	5	10
α-helix	321-323	3
β-strand	332-336	5	10
β-strand	342	1	11
α-helix	347-349	3
β-strand	356-358	3	10
β-strand	366	1	11
β-strand	378-380	3	10
β-strand	388-389	2	12
α-helix	392-394	3
β-strand	402-404	3	10
β-strand	412-413	2	12
β-strand	426-428	3	10
β-strand	447-449	3	10
β-strand	470-472	3	10
α-helix	476-480	5

Chain C: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	13
β-strand	52-56	5	13
β-strand	61-65	5	13
β-strand	72-76	5	13
β-strand	83-86	4	13
β-strand	93-96	4	13
β-strand	102-107	6	14
β-strand	110-114	5	14
β-strand	116	1	15
β-strand	118	1	15
β-strand	119-121	3	16
β-strand	124-126	3	16

Chains D and G: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	17
β-strand	52-56	5	17
β-strand	61-65	5	17
β-strand	72-76	5	17
β-strand	83-86	4	17
β-strand	93-96	4	17
β-strand	102-107	6	18
β-strand	110-114	5	18
β-strand	119-121	3	19
β-strand	124-126	3	19

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-42	4	20
β-strand	48-51	4	20
β-strand	68-72	5	20
β-strand	94-96	3	20
β-strand	118-120	3	20
β-strand	142-144	3	20
β-strand	166-168	3	20
α-helix	179-183	5
β-strand	190-192	3	20
β-strand	200-201	2	21
β-strand	214-216	3	20
β-strand	224-225	2	21
β-strand	238-240	3	20
α-helix	251-255	5
β-strand	261-263	3	20
β-strand	271-272	2	22
β-strand	285-287	3	20
β-strand	295-296	2	22
β-strand	309-313	5	23
α-helix	321-323	3
β-strand	332-336	5	23
α-helix	347-349	3
β-strand	356-358	3	23
β-strand	378-380	3	23
β-strand	388-389	2	24
α-helix	392-394	3
β-strand	402-404	3	23
β-strand	412-413	2	24
β-strand	426-428	3	23
β-strand	447-449	3	23
β-strand	470-472	3	23
α-helix	476-480	5

Chain F: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-42	4	25
β-strand	48-51	4	25
β-strand	68-72	5	25
β-strand	94-96	3	25
β-strand	118-120	3	25
β-strand	142-144	3	25
β-strand	166-168	3	25
α-helix	179-183	5
β-strand	190-192	3	25
β-strand	200-201	2	26
β-strand	214-216	3	25
β-strand	224-225	2	26
β-strand	238-240	3	25
α-helix	251-255	5
β-strand	261-263	3	25
β-strand	271-272	2	27
β-strand	285-287	3	25
β-strand	295-296	2	27
β-strand	309-313	5	28
α-helix	321-323	3
β-strand	332-336	5	28
α-helix	347-349	3
β-strand	356-358	3	28
β-strand	378-380	3	28
β-strand	388-389	2	29
α-helix	392-394	3
β-strand	402-404	3	28
β-strand	412-413	2	29
β-strand	426-428	3	28
β-strand	447-449	3	28
β-strand	470-472	3	28
α-helix	476-480	5
β-strand	540	1	28

Chain H: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	33
β-strand	52-56	5	33
β-strand	61-65	5	33
β-strand	72-76	5	33
β-strand	83-87	5	33
β-strand	92-96	5	33
β-strand	102-107	6	34
β-strand	110-114	5	34
β-strand	119-121	3	35
β-strand	124-126	3	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 5	A, B, E, F	protein	539	HOMO SAPIENS	O75473 (AlphaFold model)
R-spondin-1	C, D, G, H	protein	126	HOMO SAPIENS	Q2MKA7 (AlphaFold model)

Sequence of entity 1 (A, B, E, F), FASTA

>4BSS_1 LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 (chains A, B, E, F)
HHHHHHENLYFQGSGSSPRSGVLLRGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVF
TSYLDLSMNNISQLLPNPLPSLRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLR
HVPTEALQNLRSLQSLRLDANHISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSA
LQAMTLALNKIHHIPDYAFGNLSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLD
EFPTAIRTLSNLKELGFHSNNIRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPEL
RTLTLNGASQITEFPDLTGTANLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDL
PSFSVCQKLQKIDLRHNEIYEIKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKL
DLSSNLLSSFPITGLHGLTHLKLTGNHALQSLISSENFPELKVIEMPYAYQCCAFGVCEN
AYKISNQWNKGDNSSMDDLHKKDAGMFQAQDERDLEDFLLDFEEDLKALHSVQCSPAAA

Sequence of entity 2 (C, D, G, H), FASTA

>4BSS_2 R-SPONDIN-1 (chains C, D, G, H)
GSRISAEGSQACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARN
PDMNKCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGSSAANGTMECSSPAAA
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structure of Stem Cell Growth Factor R-Spondin 1 in Complex with the Ectodomain of its Receptor Lgr5. Peng, W.C., De Lau, W., Forneris, F. et al. Cell Rep (2013) 3:1885. DOI 10.1016/J.CELREP.2013.06.009 · 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)
4KNG 2.5 Å, Crystal structure of human LGR5-RSPO1-RNF43
4BSR 3.2 Å, Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121…
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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