4KT1: PDB entry 4KT1

Complex of R-spondin 1 with LGR4 extracellular domain. 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: 2
Atoms: 4,524
Mol. weight: 66.16 kDa
Ligands: NAG
Released: 19 Jun 2013

Explore 4KT1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KT1 contains 10 α-helices and 41 β-strands across 2 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, 31 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	1
β-strand	40-42	3	1
β-strand	61-63	3	1
β-strand	71-72	2	2
β-strand	85-87	3	1
β-strand	95-96	2	2
β-strand	109-111	3	1
β-strand	119	1	3
β-strand	133-135	3	1
β-strand	143	1	3
β-strand	157-159	3	1
α-helix	170-173	4
β-strand	181-183	3	1
β-strand	191-192	2	4
β-strand	205-207	3	1
β-strand	215-216	2	4
β-strand	229-231	3	1
α-helix	242-246	5
β-strand	252-254	3	1
β-strand	262-263	2	5
β-strand	276-278	3	1
β-strand	286-287	2	5
β-strand	300-304	5	6
β-strand	323-327	5	6
α-helix	338-341	4
β-strand	347-349	3	6
β-strand	369-371	3	6
β-strand	379-380	2	7
β-strand	393-395	3	6
β-strand	403-404	2	7
β-strand	417-419	3	6
β-strand	438-440	3	6
α-helix	449-452	4
α-helix	453-456	4
β-strand	461-463	3	6
α-helix	467-470	4
β-strand	521-523	3	6

Chain E: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	40-41	2
β-strand	44-48	5	8
β-strand	52-56	5	8
β-strand	61-65	5	8
β-strand	72-76	5	8
α-helix	79-80	2
β-strand	83-87	5	8
β-strand	92-96	5	8
α-helix	97	1
β-strand	102-107	6	9
β-strand	110-114	5	9
α-helix	118	1
β-strand	119-121	3	10
β-strand	124-126	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat-containing G-protein coupled receptor 4	A	protein	504	Homo sapiens	Q9BXB1 (AlphaFold model)
R-spondin-1	E	protein	90	Homo sapiens	Q2MKA7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4KT1_1 Leucine-rich repeat-containing G-protein coupled receptor 4 (chains A)
PPLCAAPCSCDGDRRVDCSGKGLTAVPEGLSAFTQALDISMNNITQLPEDAFKNFPFLEE
LQLAGNDLSFIHPKALSGLKELKVLTLQNNQLKTVPSEAIRGLSALQSLRLDANHITSVP
EDSFEGLVQLRHLWLDDNSLTEVPVHPLSNLPTLQALTLALNKISSIPDFAFTNLSSLVV
LHLHNNKIRSLSQHCFDGLDNLETLDLNYNNLGEFPQAIKALPSLKELGFHSNSISVIPD
GAFDGNPLLRTIHLYDNPLSFVGNSAFHNLSDLHSLVIRGASMVQQFPNLTGTVHLESLT
LTGTKISSIPNNLCQEQKMLRTLDLSYNNIRDLPSFNGCHALEEISLQRNQIYQIKEGTF
QGLISLRILDLSRNLIHEIHSRAFATLGPITNLDVSFNELTSFPTEGLNGLNQLKLVGNF
KLKEALAAKDFVNLRSLSVPYAYQCCAFWGCDSYANLNTEDNSLQDHSVAQEKGTADAAN
VTSTLENEEHSQIIIHCTPSTGHH

Sequence of entity 2 (E), FASTA

>4KT1_2 R-spondin-1 (chains E)
ACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMNKCIKCK
IEHCEACFSHNFCTKCKEGLYLHKGRCYPA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structural basis for R-spondin recognition by LGR4/5/6 receptors. Wang, D.L., Huang, B., Zhang, S. et al. Genes Dev (2013) 27:1339-1344. DOI 10.1101/gad.219360.113 · PubMed

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
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
8WVX 3.32 Å, Cryo-EM structure of LGR4 in complex with Norrin(dimer)

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