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- PDB-4li1: Crystal Structures of Lgr4 and its complex with R-spondin1 -

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Basic information

Entry
Database: PDB / ID: 4li1
TitleCrystal Structures of Lgr4 and its complex with R-spondin1
ComponentsLeucine-rich repeat-containing G-protein coupled receptor 4
KeywordsHORMONE RECEPTOR / LRR
Function / homology
Function and homology information


Regulation of FZD by ubiquitination / protein-hormone receptor activity / negative regulation of toll-like receptor signaling pathway / bone remodeling / negative regulation of cytokine production / bone mineralization / osteoblast differentiation / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / rhythmic process ...Regulation of FZD by ubiquitination / protein-hormone receptor activity / negative regulation of toll-like receptor signaling pathway / bone remodeling / negative regulation of cytokine production / bone mineralization / osteoblast differentiation / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / rhythmic process / transmembrane signaling receptor activity / spermatogenesis / G protein-coupled receptor signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
Glycoprotein hormone receptor family / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...Glycoprotein hormone receptor family / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesXenopus tropicalis
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.658 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_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

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Assembly

Deposited unit
B: Leucine-rich repeat-containing G-protein coupled receptor 4
A: Leucine-rich repeat-containing G-protein coupled receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5594
Polymers95,1162
Non-polymers4422
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich repeat-containing G-protein coupled receptor 4
hetero molecules

A: Leucine-rich repeat-containing G-protein coupled receptor 4


Theoretical massNumber of molelcules
Total (without water)95,5594
Polymers95,1162
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3530 Å2
ΔGint-5 kcal/mol
Surface area34490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.290, 158.582, 227.609
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: 47558.102 Da / Num. of mol.: 2 / Fragment: Extracellular domain residues 23-454
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: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.99 %
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: Jul 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.66→113.8 Å / Num. all: 31899 / Num. obs: 31937 / % possible obs: 99.76 % / Observed criterion σ(F): 1.77 / Observed criterion σ(I): 1.77 / Biso Wilson estimate: 64.51 Å2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.658→79.291 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7445 / SU ML: 0.45 / σ(F): 1.36 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 1609 5.05 %
Rwork0.2159 --
obs0.2188 31891 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.05 Å2 / Biso mean: 63.6731 Å2 / Biso min: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 2.658→79.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 28 174 6803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096771
X-RAY DIFFRACTIONf_angle_d1.5479206
X-RAY DIFFRACTIONf_chiral_restr0.1221093
X-RAY DIFFRACTIONf_plane_restr0.0081192
X-RAY DIFFRACTIONf_dihedral_angle_d16.6642483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6582-2.7440.42211520.335627432895100
2.744-2.84210.35421410.282726812822100
2.8421-2.95590.2851270.256427172844100
2.9559-3.09040.34381530.252227192872100
3.0904-3.25330.35191410.261127392880100
3.2533-3.45720.35351360.250727372873100
3.4572-3.72410.29811310.21127582889100
3.7241-4.09880.2831380.19127582896100
4.0988-4.69190.20731500.182760291099
4.6919-5.9110.25481800.195927682948100
5.911-79.32630.23321600.21182902306299

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