4UFR: Ectodomain of LGR5

Structure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2). Determined by X-ray diffraction at 2.2 Å resolution. Released 8 Jul 2015.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 8,912
Mol. weight: 136.65 kDa
Ligands: NAG
Released: 8 Jul 2015

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

Secondary structure: helices and β-sheets

4UFR contains 18 α-helices and 83 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: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	1
α-helix	47	1
β-strand	48-51	4	1
β-strand	68-72	5	1
α-helix	86-88	3
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	181-183	3
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	309-313	5	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
α-helix	476-482	7
β-strand	540-542	3	5

Chain B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	7
β-strand	46	1	8
β-strand	52	1	8
β-strand	55	1	7
β-strand	60-65	6	9
β-strand	70-75	6	9
α-helix	78-79	2
β-strand	82-87	6	9
β-strand	90-95	6	9
α-helix	96	1
β-strand	101-106	6	10
β-strand	109-113	5	10
α-helix	114	1
β-strand	118-120	3	11
β-strand	123-125	3	11
β-strand	135	1	11
β-strand	140	1	11

Chain C: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	39-43	5	12
β-strand	47-51	5	12
β-strand	68-72	5	12
α-helix	86-88	3
β-strand	94-96	3	12
β-strand	118-120	3	12
β-strand	142-144	3	12
β-strand	166-168	3	12
α-helix	179-182	4
β-strand	190-192	3	12
β-strand	200-201	2	13
β-strand	214-216	3	12
β-strand	224-225	2	13
β-strand	238-240	3	12
α-helix	251-255	5
β-strand	261-263	3	12
β-strand	271-272	2	14
β-strand	285-287	3	12
β-strand	295-296	2	14
β-strand	309-313	5	15
α-helix	321-323	3
β-strand	332-336	5	15
α-helix	347-350	4
β-strand	356-358	3	15
β-strand	378-380	3	15
β-strand	388-389	2	16
β-strand	402-404	3	15
β-strand	412-413	2	16
β-strand	426-428	3	15
β-strand	447-449	3	15
β-strand	470-472	3	15
α-helix	476-482	7
β-strand	540-542	3	15

Chain D: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	17
β-strand	51	1	18
β-strand	54-55	2	17
β-strand	60-65	6	18
β-strand	70-75	6	18
α-helix	78-79	2
β-strand	82-85	4	18
β-strand	92-95	4	18
β-strand	101-106	6	19
β-strand	109-113	5	19
α-helix	114	1
β-strand	118-120	3	20
β-strand	123-125	3	20
β-strand	135	1	20
β-strand	140	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 5	A, C	protein	484	HOMO SAPIENS	O75473 (AlphaFold model)
R-spondin-2	B, D	protein	120	HOMO SAPIENS	Q8BFU0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4UFR_1 LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 (chains A, C)
ETGRGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVFTSYLDLSMNNISQLLPNPLPS
LRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLRHVPTEALQNLRSLQSLRLDAN
HISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSALQAMTLALNKIHHIPDYAFGN
LSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLDEFPTAIRTLSNLKELGFHSNN
IRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPELRTLTLNGASQITEFPDLTGTA
NLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDLPSFSVCQKLQKIDLRHNEIYE
IKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKLDLSSNLLSSFPITGLHGLTHL
KLTGNHALQSLISSENFPELKVIEMPYAYQCCAFGVCENNGNNGDSVQCSPSGTHHHHHH
HHHH

Sequence of entity 2 (B, D), FASTA

>4UFR_2 R-SPONDIN-2 (chains B, D)
ETGICKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCAR
CRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMECVEGTHHHHHHHHHH

Ligands and cofactors

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

Water and common crystallization additives (CL) are not listed.

Primary citation

Crystal Structure of R-Spondin 2 in Complex with the Ectodomains of its Receptors Lgr5 and Znrf3. Zebisch, M., Jones, E.Y. J Struct Biol (2015) 191:149. DOI 10.1016/J.JSB.2015.05.008 · PubMed

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

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…
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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