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- PDB-4kng: Crystal structure of human LGR5-RSPO1-RNF43 -

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Basic information

Entry
Database: PDB / ID: 4kng
TitleCrystal structure of human LGR5-RSPO1-RNF43
Components
  • E3 ubiquitin-protein ligase RNF43
  • Leucine-rich repeat-containing G-protein coupled receptor 5
  • R-spondin-1
KeywordsSignaling Protein / Membrane Protein / Leucine-rich repeat / cysteine-rich domain / furin-repeat / protease-associated domain / ligand recognition / protein-protein interaction / N-linked glycosylation
Function / homology
Function and homology information


oocyte differentiation / Wnt receptor catabolic process / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / Signaling by RNF43 mutants / regulation of receptor internalization / frizzled binding / G protein-coupled peptide receptor activity / negative regulation of Wnt signaling pathway / inner ear development ...oocyte differentiation / Wnt receptor catabolic process / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / Signaling by RNF43 mutants / regulation of receptor internalization / frizzled binding / G protein-coupled peptide receptor activity / negative regulation of Wnt signaling pathway / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane / stem cell proliferation / G protein-coupled receptor binding / G protein-coupled receptor activity / RING-type E3 ubiquitin transferase / Wnt signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ubiquitin-protein transferase activity / transmembrane signaling receptor activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / nuclear envelope / heparin binding / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / positive regulation of protein phosphorylation / protein ubiquitination / G protein-coupled receptor signaling pathway / signaling receptor binding / endoplasmic reticulum membrane / Golgi apparatus / extracellular space / extracellular region / nucleoplasm / nucleus / metal ion binding / plasma membrane
Similarity search - Function
E3 ubiquitin-protein ligase RNF43, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / : / Glycoprotein hormone receptor family / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 ...E3 ubiquitin-protein ligase RNF43, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / : / Glycoprotein hormone receptor family / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Glucose Oxidase; domain 1 - #30 / Ring finger domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Glucose Oxidase; domain 1 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Furin-like repeat / Furin-like repeats / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Growth factor receptor cysteine-rich domain superfamily / Ring finger / Leucine-rich repeat / 3-Layer(bba) Sandwich / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ribbon / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Zinc finger, RING/FYVE/PHD-type / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Leucine-rich repeat-containing G-protein coupled receptor 5 / R-spondin-1 / E3 ubiquitin-protein ligase RNF43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsChen, P.H. / He, X.
CitationJournal: Genes Dev. / Year: 2013
Title: The structural basis of R-spondin recognition by LGR5 and RNF43.
Authors: Chen, P.H. / Chen, X. / Lin, Z. / Fang, D. / He, X.
History
DepositionMay 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Data collection
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat-containing G-protein coupled receptor 5
B: Leucine-rich repeat-containing G-protein coupled receptor 5
M: R-spondin-1
P: R-spondin-1
E: E3 ubiquitin-protein ligase RNF43
F: E3 ubiquitin-protein ligase RNF43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,8839
Polymers178,3826
Non-polymers5013
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.575, 120.971, 181.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12M
22P
13E
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSERAA30 - 5421 - 513
21GLYGLYSERSERBB30 - 5421 - 513
12CYSCYSGLYGLYMC40 - 1328 - 100
22CYSCYSGLYGLYPD40 - 1328 - 100
13GLNGLNGLUGLUEE44 - 1903 - 149
23GLNGLNGLUGLUFF44 - 1903 - 149

NCS ensembles :
ID
1
2
3
Details0.009563 0.000000 0.000000 0.00000 0.000000 0.008266 0.000000 0.00000 0.000000 0.000000 0.005525 0.00000

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Components

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Protein , 3 types, 6 molecules ABMPEF

#1: Protein Leucine-rich repeat-containing G-protein coupled receptor 5 / G-protein coupled receptor 49 / G-protein coupled receptor 67 / G-protein coupled receptor HG38


Mass: 59278.367 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGR5, GPR49, GPR67 / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O75473
#2: Protein R-spondin-1 / Roof plate-specific spondin-1 / hRspo1


Mass: 12362.315 Da / Num. of mol.: 2 / Fragment: furin repeats
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSPO1 / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q2MKA7
#3: Protein E3 ubiquitin-protein ligase RNF43 / RING finger protein 43


Mass: 17550.203 Da / Num. of mol.: 2 / Fragment: PA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF43 / Plasmid: PVLAD6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q68DV7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Sugars , 1 types, 2 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 206 molecules

#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG4000, 0.2M ammonium sulfate, 7% Sucrose and 0.1 M TRIS pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2012
RadiationMonochromator: Ni / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→39.51 Å / Num. all: 74020 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-3000data collection
X-PLORmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→39.51 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.435 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27633 3894 5 %RANDOM
Rwork0.23197 ---
obs0.23425 74020 97.08 %-
all-74020 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.177 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11012 0 29 205 11246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911321
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210961
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.98415435
X-RAY DIFFRACTIONr_angle_other_deg1.1513.00425227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.88251405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.78424.534483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.212151947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8111558
X-RAY DIFFRACTIONr_chiral_restr0.1020.21763
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112681
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022497
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6657.445647
X-RAY DIFFRACTIONr_mcbond_other5.6617.4395646
X-RAY DIFFRACTIONr_mcangle_it8.75611.1317043
X-RAY DIFFRACTIONr_scbond_it5.3627.8385674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A274560.14
12B274560.14
21M48110.12
22P48110.12
31E76890.18
32F76890.18
LS refinement shellResolution: 2.498→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 241 -
Rwork0.382 5121 -
obs--91.89 %

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