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- PDB-4ufr: Structure of the ectodomain of LGR5 in complex with R-spondin-2 (... -

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Basic information

Entry
Database: PDB / ID: 4ufr
TitleStructure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2)
Components
  • LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
  • R-SPONDIN-2
KeywordsSIGNALING PROTEIN / WNT / LGR / RSPO
Function / homology
Function and homology information


trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / G protein-coupled peptide receptor activity / embryonic forelimb morphogenesis ...trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / G protein-coupled peptide receptor activity / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / epithelial tube branching involved in lung morphogenesis / bone mineralization / inner ear development / hair follicle development / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / heparin binding / regulation of cell population proliferation / G protein-coupled receptor signaling pathway / signaling receptor binding / Golgi apparatus / cell surface / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Spondin-like TSP1 domain / Spondin-like TSP1 domain / 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 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain ...Spondin-like TSP1 domain / Spondin-like TSP1 domain / 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 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / 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 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribbon / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat-containing G-protein coupled receptor 5 / R-spondin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal Structure of R-Spondin 2 in Complex with the Ectodomains of its Receptors Lgr5 and Znrf3.
Authors: Zebisch, M. / Jones, E.Y.
History
DepositionMar 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Structure summary
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Sep 23, 2015Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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: R-SPONDIN-2
C: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
D: R-SPONDIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,65412
Polymers135,9984
Non-polymers6558
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-74.7 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.148, 59.777, 112.210
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 / G-PROTEIN COUPLED RECEPTOR 49 / G-PROTEIN COUPLED RECEPTOR 6 7 / G-PROTEIN COUPLED RECEPTOR HG38 / LGR5


Mass: 54052.348 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544
Source method: isolated from a genetically manipulated source
Details: UNSTRUCTURED LOOP REPLACED WITH SHORT LINKER, A488-H537 TO NGNNGD
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: O75473
#2: Protein R-SPONDIN-2 / CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2 / CRISTIN-2 / MCRISTIN-2 / ROOF ...CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2 / CRISTIN-2 / MCRISTIN-2 / ROOF PLATE-SPECIFIC SPONDIN-2 / RSPO2


Mass: 13946.869 Da / Num. of mol.: 2 / Fragment: FU1-FU2, RESIDUES 39-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BFU0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5.5
Details: 25 %W/V PEG3350, 0.200 M LITHIUM SULPHATE, 0.100 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.009
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.2→69 Å / Num. obs: 62167 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→110.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 23.344 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26172 1184 1.9 %RANDOM
Rwork0.20805 ---
obs0.20909 60900 90.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.664 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20.71 Å2
2--0.18 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→110.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8722 0 34 150 8906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198977
X-RAY DIFFRACTIONr_bond_other_d0.0010.028478
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.97312200
X-RAY DIFFRACTIONr_angle_other_deg0.847319507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48951117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8724.141396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.511151498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.661549
X-RAY DIFFRACTIONr_chiral_restr0.0880.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022090
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_it1.8693.0794480
X-RAY DIFFRACTIONr_mcbond_other1.8683.0784479
X-RAY DIFFRACTIONr_mcangle_it2.9374.6115590
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4363.3184497
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 50 -
Rwork0.362 2902 -
obs--59.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3197-0.74823.07380.66150.19954.55960.183-0.0497-0.6914-0.1047-0.01430.09990.7463-0.1314-0.16880.3914-0.00630.05630.06940.00810.116717.065-15.681819.9634
21.54540.21170.37563.32860.84792.4839-0.0154-0.0960.00440.02220.0931-0.47330.06290.287-0.07770.2310.06790.03260.0936-0.00360.074135.76961.648534.418
31.7083-1.13-1.66933.5521.63954.98920.0459-0.07320.24650.11350.0078-0.4782-0.34870.3426-0.05370.4017-0.0542-0.01620.0594-0.01670.121726.047431.758854.421
42.7159-3.1743-0.74663.99832.0788.0626-0.134-0.1704-0.32050.2576-0.05830.5994-0.1951-1.47870.19230.62160.04120.2090.3162-0.05660.47595.376735.258666.9096
57.3357-1.1795-0.11876.2619-1.38128.7004-0.0228-0.009-0.4278-0.13870.00121.37820.2455-0.93980.02160.46460.071-0.04490.3651-0.13810.379310.18-3.676439.7267
65.78311.38610.574810.9324-5.608111.9458-0.47290.81881.5264-0.7387-0.05090.1498-0.9896-0.82180.52380.51980.1642-0.11210.46630.07320.498921.525611.219920.042
78.6115-0.6118-0.60641.33370.42222.89210.00770.07380.9316-0.11580.10560.215-0.6409-0.2711-0.11330.3584-0.02580.06210.07420.02420.1838-5.148257.672899.7174
81.867-1.5735-1.48913.78471.41522.0288-0.0596-0.24930.22810.29340.2767-0.5168-0.04680.4174-0.21710.2778-0.11070.05590.1298-0.0810.107818.279239.667498.3443
91.1185-0.1157-0.75942.93191.85175.17750.1002-0.059-0.17860.26110.015-0.17990.35340.3808-0.11520.2989-0.0050.06880.0369-0.01310.096220.12189.616676.0356
104.73040.8986-2.23670.60960.92079.69860.1770.5586-0.191-0.1927-0.0990.22070.4153-1.3481-0.0780.6395-0.024-0.24760.2237-0.0760.46558.70916.14954.5563
118.07811.23252.41827.60040.43979.9979-0.05480.50990.1981-0.79470.00190.8163-0.0312-0.75650.05290.3218-0.05840.05320.2594-0.08080.1887-0.556245.437580.3934
128.9433.4268-3.300111.9907-6.459212.12230.0018-0.6288-1.50760.5230.26780.3790.8055-1.1687-0.26960.4729-0.13070.0290.42080.05360.4693-0.862430.4999102.7827
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2A130 - 291
3X-RAY DIFFRACTION3A292 - 437
4X-RAY DIFFRACTION4A438 - 544
5X-RAY DIFFRACTION5B40 - 95
6X-RAY DIFFRACTION6B96 - 141
7X-RAY DIFFRACTION7C1 - 129
8X-RAY DIFFRACTION8C130 - 291
9X-RAY DIFFRACTION9C292 - 437
10X-RAY DIFFRACTION10C438 - 544
11X-RAY DIFFRACTION11D40 - 95
12X-RAY DIFFRACTION12D96 - 141

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