4BST: Ectodomain of LGR5

Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P6122 crystal form. Determined by X-ray diffraction at 4.3 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 4.3 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 8,833
Mol. weight: 149.62 kDa
Ligands: NAG
Released: 19 Jun 2013

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

Secondary structure: helices and β-sheets

4BST contains 27 α-helices and 85 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: 12 helices, 29 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
α-helix	108-110	3
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
α-helix	273	1
β-strand	285-287	3	1
β-strand	295-296	2	4
α-helix	299-301	3
β-strand	309-313	5	5
α-helix	321-323	3
β-strand	332-336	5	5
α-helix	345-350	6
β-strand	356-358	3	5
β-strand	378-380	3	5
β-strand	388-389	2	6
α-helix	392-394	3
β-strand	402-404	3	5
β-strand	412-413	2	6
α-helix	415-418	4
β-strand	426-428	3	5
β-strand	447-449	3	5
β-strand	470-472	3	5
α-helix	476-479	4
α-helix	480-482	3
β-strand	540-542	3	5

Chain B: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-42	4	7
β-strand	48-51	4	7
β-strand	68-72	5	7
β-strand	94-96	3	7
α-helix	108-110	3
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
α-helix	273	1
β-strand	285-287	3	7
β-strand	295-296	2	10
β-strand	309	1	11
β-strand	312	1	12
α-helix	321-323	3
β-strand	332-334	3	11
β-strand	335	1	12
α-helix	347-350	4
β-strand	356-358	3	11
β-strand	378-380	3	11
β-strand	388-389	2	13
α-helix	392-394	3
β-strand	402-404	3	11
β-strand	412-413	2	13
α-helix	415-418	4
β-strand	426-428	3	11
β-strand	447-449	3	11
β-strand	470-472	3	11
α-helix	476-479	4
α-helix	480-482	3
β-strand	540-542	3	11

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	41	1	14
β-strand	44-48	5	14
β-strand	52-56	5	14
β-strand	61-66	6	14
β-strand	71-76	6	14
α-helix	79-80	2
β-strand	81	1	14
β-strand	83-86	4	14
β-strand	93-96	4	14
β-strand	102-105	4	15
β-strand	111-114	4	15
α-helix	115	1
β-strand	119-121	3	16
β-strand	124-126	3	16

Chain D: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	17
β-strand	52-56	5	17
β-strand	61-63	3	18
β-strand	66	1	19
β-strand	71	1	19
β-strand	73	1	17
β-strand	74-76	3	18
α-helix	79-80	2
β-strand	83-86	4	18
β-strand	93-96	4	18
β-strand	102-105	4	20
β-strand	111-114	4	20
α-helix	115	1
β-strand	119-121	3	21
β-strand	124-126	3	21

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>4BST_1 LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 (chains A, B)
HHHHHHENLYFQGSGSSPRSGVLLRGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVF
TSYLDLSMNNISQLLPNPLPSLRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLR
HVPTEALQNLRSLQSLRLDANHISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSA
LQAMTLALNKIHHIPDYAFGNLSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLD
EFPTAIRTLSNLKELGFHSNNIRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPEL
RTLTLNGASQITEFPDLTGTANLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDL
PSFSVCQKLQKIDLRHNEIYEIKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKL
DLSSNLLSSFPITGLHGLTHLKLTGNHALQSLISSENFPELKVIEMPYAYQCCAFGVCEN
AYKISNQWNKGDNSSMDDLHKKDAGMFQAQDERDLEDFLLDFEEDLKALHSVQCSPAAA

Sequence of entity 2 (C, D), FASTA

>4BST_2 R-SPONDIN-1 (chains C, D)
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…
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…
4UFS 4.8 Å, Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5…

Browse structure collections

About this viewer

MolViewer shows 4BST directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.