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- PDB-4qxf: crystal structure of human LGR4 and Rspo1 -

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Basic information

Entry
Database: PDB / ID: 4qxf
Titlecrystal structure of human LGR4 and Rspo1
Components
  • Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B
  • R-spondin-1
KeywordsMEMBRANE PROTEIN / ligand-receptor complex / LRR repeats / Beta-Hairpins / Glucosylation / Cell Membrane
Function / homology
Function and homology information


metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / intestinal stem cell homeostasis / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling ...metanephric glomerulus development / metanephric nephron tubule morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / protein-hormone receptor activity / intestinal stem cell homeostasis / regulation of receptor internalization / negative regulation of toll-like receptor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / male genitalia development / bone remodeling / G protein-coupled peptide receptor activity / digestive tract development / negative regulation of cold-induced thermogenesis / negative regulation of cytokine production / bone mineralization / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / hormone-mediated signaling pathway / G protein-coupled receptor activity / G protein-coupled receptor binding / circadian regulation of gene expression / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / heparin binding / spermatogenesis / positive regulation of protein phosphorylation / signaling receptor binding / innate immune response / extracellular region / membrane / nucleus / plasma membrane
Similarity search - Function
R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / 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 ...R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / 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, SDS22-like subfamily / 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
Similarity search - Domain/homology
R-spondin-1 / Variable lymphocyte receptor B / Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsXu, J.G. / Huang, C. / Zhou, Y. / Zhu, Y.
CitationJournal: TO BE PUBLISHED
Title: crystal structure of human LGR4 and Rspo1
Authors: Xu, J.G. / Huang, C. / Zhou, Y. / Zhu, Y.
History
DepositionJul 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 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

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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 4, Variable lymphocyte receptor B
B: Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B
E: R-spondin-1
C: R-spondin-1


Theoretical massNumber of molelcules
Total (without water)88,6744
Polymers88,6744
Non-polymers00
Water4,738263
1
A: Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

C: R-spondin-1


Theoretical massNumber of molelcules
Total (without water)44,3372
Polymers44,3372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area1780 Å2
ΔGint-2 kcal/mol
Surface area18170 Å2
MethodPISA
2
B: Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B
E: R-spondin-1


Theoretical massNumber of molelcules
Total (without water)44,3372
Polymers44,3372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-3 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.867, 137.913, 82.560
Angle α, β, γ (deg.)90.00, 100.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B / G-protein coupled receptor 48


Mass: 33151.766 Da / Num. of mol.: 2 / Fragment: UNP residues 27-252, UNP residues 128-200 / Mutation: D75G
Source method: isolated from a genetically manipulated source
Details: chimera of (Leucine-rich repeat-containing G-protein coupled receptor 4 and Variable lymphocyte receptor B)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: GPR48, LGR4, VLRB / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9BXB1, UniProt: Q4G1L2
#2: Protein R-spondin-1 / Roof plate-specific spondin-1 / hRspo1


Mass: 11185.049 Da / Num. of mol.: 2 / Fragment: UNP residues 34-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSPO1 / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q2MKA7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 0.2M sodium thiocyanate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 44255 / Num. obs: 43609 / % possible obs: 98.54 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.25-2.33198.3
2.33-3.85199.3
3.85-4.85199
4.8-50196.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXE

4qxe


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.743 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24268 2319 5 %RANDOM
Rwork0.21325 ---
all0.21474 44255 --
obs0.21474 43609 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.16 Å2
2--0.74 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5859 0 0 263 6122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9878197
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0545754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53825252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.987151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5731528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214502
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3271.53797
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68526135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28232236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1384.52061
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: 2.253→2.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 160 -
Rwork0.221 3053 -
obs--94.44 %
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)
15.21342.17591.80695.83061.7955.22310.4203-0.8668-0.43380.98440.0215-0.55450.45920.2827-0.44180.39630.0397-0.07040.28710.06260.2444-9.63227.678510.4067
24.3112-0.4892.21243.46940.10935.4205-0.0187-0.3087-0.07540.26880.09250.06040.1071-0.1544-0.07380.07060.00130.0060.08040.04110.058-16.878716.35446.1725
31.62750.5777-0.55372.0437-1.0133.28350.03180.03270.1772-0.03040.08280.1592-0.1505-0.1983-0.11460.01760.0177-0.01410.0284-0.01160.065-12.172129.5102-11.9429
43.84860.2134-0.43462.49920.51994.56550.00020.40540.3424-0.44020.0208-0.1334-0.37070.0757-0.0210.18960.01530.04670.16570.030.14063.772432.7832-34.2344
51.3111-1.0043-2.53374.52062.47874.99610.10820.07810.1949-0.45750.3173-0.6821-0.2675-0.0101-0.42550.2729-0.06560.03820.37870.03320.31524.384584.8124-54.4247
60.82460.0097-0.26312.4234-1.77693.3802-0.01920.21860.0094-0.26760.16040.25160.1221-0.2159-0.14120.0432-0.0441-0.01290.1211-0.01460.0913-6.650269.6851-39.1922
76.0388-2.8352-1.97617.31243.2195.66790.0278-0.092-0.33570.3597-0.12030.31440.2115-0.24390.09250.1194-0.0312-0.02460.05460.02710.0427-6.058860.7757-18.303
82.7189-0.98170.16512.96650.28784.3484-0.0914-0.1973-0.2510.60080.0507-0.10340.42990.05240.04070.2207-0.0317-0.01230.09150.00560.13621.675561.3734-5.7397
92.7929-1.54141.2688.4215-1.98523.36150.0938-0.1006-0.3040.2113-0.1149-0.30880.54380.09120.02110.2594-0.0307-0.02650.2453-0.01360.2485-0.386779.357713.6316
1016.4763.36257.09243.7660.22766.297-0.13060.37520.5847-0.3422-0.14930.0575-0.0933-0.03850.27980.0684-0.0041-0.00740.1335-0.00260.1268-8.481496.09222.4536
117.7926-0.29241.750911.72680.28928.5063-0.09250.2340.6553-0.0576-0.11980.0238-0.88870.43710.21230.2988-0.0513-0.03250.30640.02670.19155.691885.9354-26.6646
1214.55850.3529-4.53198.0258-2.20893.8675-0.00330.01990.0125-0.0177-0.0747-0.6582-0.06160.43160.0780.0386-0.0299-0.0060.1771-0.02240.15414.453566.2766-33.05
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 52
2X-RAY DIFFRACTION2A53 - 103
3X-RAY DIFFRACTION3A104 - 236
4X-RAY DIFFRACTION4A237 - 324
5X-RAY DIFFRACTION5B25 - 58
6X-RAY DIFFRACTION6B59 - 212
7X-RAY DIFFRACTION7B213 - 240
8X-RAY DIFFRACTION8B241 - 325
9X-RAY DIFFRACTION9C52 - 109
10X-RAY DIFFRACTION10C110 - 130
11X-RAY DIFFRACTION11E53 - 99
12X-RAY DIFFRACTION12E100 - 130

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