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- PDB-4kt1: Complex of R-spondin 1 with LGR4 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 4kt1
TitleComplex of R-spondin 1 with LGR4 extracellular domain
Components
  • Leucine-rich repeat-containing G-protein coupled receptor 4
  • R-spondin-1
KeywordsHORMONE RECEPTOR/CELL ADHESION / R-spondin / LGR receptor / complex structure / Wnt signaling / HORMONE RECEPTOR-CELL ADHESION complex
Function / homology
Function and homology information


cell differentiation involved in metanephros development / 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 ...cell differentiation involved in metanephros development / 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 / G protein-coupled receptor binding / G protein-coupled receptor activity / circadian regulation of gene expression / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / transmembrane signaling receptor activity / heparin binding / spermatogenesis / positive regulation of protein phosphorylation / signaling receptor binding / innate immune response / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / extracellular region / 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 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Thrombospondin type-1 (TSP1) repeat superfamily ...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 / Leucine-rich repeats, bacterial type / 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 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
R-spondin-1 / Leucine-rich repeat-containing G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsWang, X.Q. / Wang, D.L.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural basis for R-spondin recognition by LGR4/5/6 receptors
Authors: Wang, D.L. / Huang, B. / Zhang, S. / Yu, X. / Wu, W. / Wang, X.Q.
History
DepositionMay 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: 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_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: R-spondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1654
Polymers65,5192
Non-polymers6462
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.376, 91.376, 87.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 55438.344 Da / Num. of mol.: 1 / Fragment: UNP residues 26-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGR4 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXB1
#2: Protein R-spondin-1 / Roof plate-specific spondin-1 / hRspo1


Mass: 10080.942 Da / Num. of mol.: 1 / Fragment: UNP residues 39-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSPO1 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2MKA7
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.497→50 Å / Num. all: 28261 / Num. obs: 28261 / % possible obs: 99.9 % / Observed criterion σ(F): 1.96 / Observed criterion σ(I): 1.96 / Biso Wilson estimate: 35.06 Å2
Reflection shellResolution: 2.5→2.56 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZYO

3zyo


Resolution: 2.497→24.671 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8596 / SU ML: 0.26 / σ(F): 1.96 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1428 5.05 %RANDOM
Rwork0.1601 ---
all0.1626 28261 --
obs0.1626 28261 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.64 Å2 / Biso mean: 41.7028 Å2 / Biso min: 17.17 Å2
Refinement stepCycle: LAST / Resolution: 2.497→24.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 42 217 4524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074411
X-RAY DIFFRACTIONf_angle_d1.1595972
X-RAY DIFFRACTIONf_chiral_restr0.077694
X-RAY DIFFRACTIONf_plane_restr0.004774
X-RAY DIFFRACTIONf_dihedral_angle_d15.4951631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4969-2.58610.27821320.215126982830
2.5861-2.68950.26721550.203627022857
2.6895-2.81180.26811370.184226662803
2.8118-2.95980.25811210.190127012822
2.9598-3.14490.25911550.186526732828
3.1449-3.38710.21441410.178426972838
3.3871-3.72690.19651410.149126792820
3.7269-4.26380.18471480.132126542802
4.2638-5.36290.17391560.131226872843
5.3629-24.67190.17731420.15426762818
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6609-0.5917-0.03331.6182-0.14170.4837-0.0142-0.0001-0.0390.06420.0067-0.0442-0.0432-0.01340.2758-0.0191-0.00670.2637-0.01890.216350.538165.8299-0.1996
20.7882-0.56520.13011.24250.29941.1656-0.1612-0.0418-0.0570.1599-0.00640.1570.149-0.45810.4005-0.00960.01110.3609-0.00170.350847.030851.02539.0301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA26 - 529
2X-RAY DIFFRACTION2CHAIN EE39 - 128

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