Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 150.23 kDa 
• Atom Count: 9274 
• Modelled Residue Count: 1170 
• Deposited Residue Count: 1330 
• Unique protein chains: 2

4BSR

Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121 crystal form

• PDB DOI: 10.2210/pdb4BSR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-11 Released: 2013-06-19 
• Deposition Author(s): Peng, W.C., de Lau, W., Forneris, F., Granneman, J.C.M., Huch, M., Clevers, H., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Literature

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., Granneman, J.C.M., Huch, M., Clevers, H., Gros, P.

(2013) Cell Rep 3: 1885

• PubMed: 23809763 
• DOI: 10.1016/j.celrep.2013.06.009
• Primary Citation of Related Structures:  
  4BSO, 4BSP, 4BSR, 4BSS, 4BST, 4BSU


• PubMed Abstract: 
  

Leucine-rich repeat-containing G protein-coupled receptors 4-6 (LGR4-LGR6) are receptors for R-spondins, potent Wnt agonists that exert profound trophic effects on Wnt-driven stem cells compartments. We present crystal structures of a signaling-competent fragment of R-spondin 1 (Rspo1) at a resolution of 2.0 Å and its complex with the LGR5 ectodomain at a resolution of 3.2 Å. Ecto-LGR5 binds Rspo1 at its concave leucine-rich-repeat (LRR) surface, forming a dimeric 2:2 complex. Fully conserved residues on LGR4-LGR6 explain promiscuous binding of R-spondins. A phenylalanine clamp formed by Rspo1 Phe106 and Phe110 pinches Ala190 of LGR5 and is critical for binding. Mutations related to congenital anonychia reduce signaling, but not binding of Rspo1 to LGR5. Furthermore, antibody binding to the extended loop of the C-terminal LRR cap of LGR5 activates signaling in a ligand-independent manner. Thus, our data reveal binding of R-spondins to conserved sites on LGR4-LGR6 and, in analogy to FSHR and related receptors, suggest a direct signaling role for LGR4-LGR6 in addition to its formation of Wnt receptor and coreceptor complexes.

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Organizational Affiliation: 

Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5	A, B	539	Homo sapiens	Mutation(s): 0  Gene Names: LGR5, GPR49, GPR67
UniProt & NIH Common Fund Data Resources
Find proteins for O75473 (Homo sapiens) Explore O75473  Go to UniProtKB:  O75473
PHAROS:  O75473

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
R-SPONDIN-1	C, D	126	Homo sapiens	Mutation(s): 0  Gene Names: RSPO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2MKA7 (Homo sapiens) Explore Q2MKA7  Go to UniProtKB:  Q2MKA7
PHAROS:  Q2MKA7

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.175	α = 90
b = 143.779	β = 90
c = 167.338	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-11 
• Released Date: 2013-06-19 
Deposition Author(s): Peng, W.C., de Lau, W., Forneris, F., Granneman, J.C.M., Huch, M., Clevers, H., Gros, P.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary