4KNG

Crystal structure of human LGR5-RSPO1-RNF43

PDB DOI: https://doi.org/10.2210/pdb4KNG/pdb

Classification: Signaling Protein, Membrane Protein
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

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

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

Ligand Structure Quality Assessment

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

PubMed: 23756651 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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 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.

Macromolecule Content

Total Structure Weight: 178.88 kDa
Atom Count: 11,252
Modelled Residue Count: 1,413
Deposited Residue Count: 1,612
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat-containing G-protein coupled receptor 5	A, B	531	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 GTEx: ENSG00000139292
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75473
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
R-spondin-1	C [auth M], D [auth P]	115	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 GTEx: ENSG00000169218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2MKA7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF43	E, F	160	Homo sapiens	Mutation(s): 0 Gene Names: RNF43 EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q68DV7 (Homo sapiens) Explore Q68DV7 Go to UniProtKB: Q68DV7
PHAROS: Q68DV7 GTEx: ENSG00000108375
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68DV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B]	G [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

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 = 104.575	α = 90
b = 120.971	β = 90
c = 181.009	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
X-PLOR	model building
REFMAC	refinement
HKL-3000	data reduction
SCALA	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-19

Deposition Author(s):

Chen, P.H.

He, X.

Revision History (Full details and data files)

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