4KNG

Crystal structure of human LGR5-RSPO1-RNF43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structural basis of R-spondin recognition by LGR5 and RNF43.

Chen, P.H.Chen, X.Lin, Z.Fang, D.He, X.

(2013) Genes Dev. 27: 1345-1350

  • DOI: 10.1101/gad.219915.113

  • PubMed Abstract: 
  • R-spondins (RSPOs) enhance Wnt signaling, affect stem cell behavior, bind to leucine-rich repeat-containing G-protein-coupled receptors 4-6, (LGR4-6) and the transmembrane E3 ubiquitin ligases RING finger 43/zinc and RING finger 3 (RNF43/ZNRF3). The ...

    R-spondins (RSPOs) enhance Wnt signaling, affect stem cell behavior, bind to leucine-rich repeat-containing G-protein-coupled receptors 4-6, (LGR4-6) and the transmembrane E3 ubiquitin ligases RING finger 43/zinc and RING finger 3 (RNF43/ZNRF3). The structure of RSPO1 bound to both LGR5 and RNF43 ectodomains confirms their physical linkage. RSPO1 is sandwiched by LGR5 and RNF43, with its rod module of the cysteine-rich domain (CRD) contacting LGR5 and a hairpin inserted into RNF43. LGR5 does not contact RNF43 but increases the affinity of RSPO1 to RNF43, supporting LGR5 as an engagement receptor and RNF43 as an effector receptor. Disease mutations map to the RSPO1-RNF43 interface, which promises therapeutic targeting.


    Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucine-rich repeat-containing G-protein coupled receptor 5
A, B
531Homo sapiensMutation(s): 0 
Gene Names: LGR5 (GPR49, GPR67)
Find proteins for O75473 (Homo sapiens)
Go to Gene View: LGR5
Go to UniProtKB:  O75473
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
R-spondin-1
M, P
115Homo sapiensMutation(s): 0 
Gene Names: RSPO1
Find proteins for Q2MKA7 (Homo sapiens)
Go to Gene View: RSPO1
Go to UniProtKB:  Q2MKA7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF43
E, F
160Homo sapiensMutation(s): 0 
Gene Names: RNF43
EC: 2.3.2.27
Find proteins for Q68DV7 (Homo sapiens)
Go to Gene View: RNF43
Go to UniProtKB:  Q68DV7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.575α = 90.00
b = 120.971β = 90.00
c = 181.009γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
X-PLORmodel building
HKL-3000data collection
HKL-3000data reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-05-09 
  • Released Date: 2013-06-19 
  • Deposition Author(s): Chen, P.H., He, X.

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Data collection
  • Version 1.2: 2013-07-24
    Type: Database references