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- PDB-4li2: Crystal Structures of Lgr4 and its complex with R-spondin1 -

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Basic information

Entry
Database: PDB / ID: 4li2
TitleCrystal Structures of Lgr4 and its complex with R-spondin1
Components
  • Leucine-rich repeat-containing G-protein coupled receptor 4
  • R-spondin-1
KeywordsHormone Receptor/Signaling protein / LRR / Hormone Receptor-Signaling protein complex
Function / homology
Function and homology information


Regulation of FZD by ubiquitination / protein-hormone receptor activity / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / bone remodeling / negative regulation of cytokine production / bone mineralization / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / G protein-coupled receptor binding ...Regulation of FZD by ubiquitination / protein-hormone receptor activity / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / bone remodeling / negative regulation of cytokine production / bone mineralization / positive regulation of Wnt signaling pathway / Regulation of FZD by ubiquitination / G protein-coupled receptor binding / Wnt signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / heparin binding / spermatogenesis / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
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 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat ...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 / 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, 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 4 / R-spondin-1
Similarity search - Component
Biological speciesXenopus tropicalis
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsXu, Y. / Rajashankar, K. / Robev, D.
CitationJournal: Structure / Year: 2013
Title: Crystal structures of lgr4 and its complex with R-spondin1.
Authors: Xu, K. / Xu, Y. / Rajashankar, K.R. / Robev, D. / Nikolov, D.B.
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich repeat-containing G-protein coupled receptor 4
B: R-spondin-1


Theoretical massNumber of molelcules
Total (without water)59,6952
Polymers59,6952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.379, 160.923, 82.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsbiological unit is the same as asym.

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Components

#1: Protein Leucine-rich repeat-containing G-protein coupled receptor 4


Mass: 47542.035 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN RESIDUES 23-454 / Mutation: C223S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog)
Gene: lgr4 / Plasmid: pCDNA3.1 / Cell line (production host): HEK293 CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: B0BLW3
#2: Protein R-spondin-1 / Roof plate-specific spondin-1 / hRspo1


Mass: 12153.070 Da / Num. of mol.: 1 / Fragment: FU 1 and FU 2 repeat residues 33-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: R-spondin1, RSPO1 / Plasmid: pCDNA3.1 / Cell line (production host): HEK293 CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: Q2MKA7
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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.7
Details: 22% PEG3350, 200 mM MgCl2 and 100 mM BisTris pH 5.7, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11577 / % possible obs: 98.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 93.49 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.704 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.314.40.96611480.483199
3.31-3.454.20.61111320.495199.2
3.45-3.64.40.43911550.521198.5
3.6-3.794.70.26311390.589199.3
3.79-4.034.50.16611530.702199.5
4.03-4.344.50.12611580.802198.4
4.34-4.784.30.08811330.912198.1
4.78-5.474.60.0711780.8199.2
5.47-6.894.30.0611660.798197.3
6.89-504.30.03612150.933196.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LI1

4li1


Resolution: 3.19→47.613 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6885 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 35.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 1155 10.01 %
Rwork0.2292 --
obs0.2347 11539 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.17 Å2 / Biso mean: 71.1696 Å2 / Biso min: 23.53 Å2
Refinement stepCycle: LAST / Resolution: 3.19→47.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 0 0 4027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014118
X-RAY DIFFRACTIONf_angle_d1.55575
X-RAY DIFFRACTIONf_chiral_restr0.113649
X-RAY DIFFRACTIONf_plane_restr0.007726
X-RAY DIFFRACTIONf_dihedral_angle_d17.5541510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1896-3.33480.43511400.36011260140097
3.3348-3.51050.38251400.28661271141198
3.5105-3.73040.31491460.24021297144399
3.7304-4.01830.26621440.20991285142999
4.0183-4.42240.30161430.18891294143798
4.4224-5.06170.22631440.18811305144998
5.0617-6.37480.27811460.25221313145998
6.3748-47.61830.26681520.22771359151197

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