4KNG

Crystal structure of human LGR5-RSPO1-RNF43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    4KNG

  • 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 stru ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine-rich repeat-containing G-protein coupled receptor 5 AB531Homo sapiensMutation(s): 0 
Gene Names: LGR5GPR49GPR67
Find proteins for O75473 (Homo sapiens)
Explore O75473 
Go to UniProtKB:  O75473
NIH Common Fund Data Resources
PHAROS:  O75473
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
R-spondin-1 MP115Homo sapiensMutation(s): 0 
Gene Names: RSPO1
Find proteins for Q2MKA7 (Homo sapiens)
Explore Q2MKA7 
Go to UniProtKB:  Q2MKA7
NIH Common Fund Data Resources
PHAROS:  Q2MKA7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF43 EF160Homo sapiensMutation(s): 0 
Gene Names: RNF43
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q68DV7 (Homo sapiens)
Explore Q68DV7 
Go to UniProtKB:  Q68DV7
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PHAROS:  Q68DV7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.575α = 90
b = 120.971β = 90
c = 181.009γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
X-PLORmodel building
REFMACrefinement
HKL-3000data reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

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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
    Changes: Data collection
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary