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- PDB-4bst: Structure of the ectodomain of LGR5 in complex with R-spondin-1 (... -

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Basic information

Entry
Database: PDB / ID: 4bst
TitleStructure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P6122 crystal form
Components
  • LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
  • R-SPONDIN-1
KeywordsSIGNALING PROTEIN / ADULT STEM CELL / LEUCINE-RICH REPEAT G-PROTEIN COUPLED RECEPTOR / LEUCINE-RICH REPEAT / FURIN DOMAIN / WNT SIGNALING / CONGENITAL ANONYCHIA
Function / homology
Function and homology information


epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / regulation of receptor internalization / G protein-coupled peptide receptor activity / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane ...epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / regulation of receptor internalization / G protein-coupled peptide receptor activity / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / heparin binding / regulation of cell population proliferation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding / Golgi apparatus / extracellular region / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / 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 ...R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / 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 Repeat / Leucine-rich repeats, bacterial type / 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 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Leucine-rich repeat-containing G-protein coupled receptor 5 / R-spondin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 4.3 Å
AuthorsPeng, W.C. / de Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
CitationJournal: Cell Rep. / Year: 2013
Title: Structure of Stem Cell Growth Factor R-Spondin 1 in Complex with the Ectodomain of its Receptor Lgr5.
Authors: Peng, W.C. / De Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
History
DepositionJun 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _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_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
C: R-SPONDIN-1
D: R-SPONDIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6189
Polymers148,1464
Non-polymers1,4715
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-11.9 kcal/mol
Surface area49300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.100, 131.100, 531.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 / LGR5 / G-PROTEIN COUPLED RECEPTOR 49 / G-PROTEIN COUPLED RECEPTOR 67 / G-PROTEIN COUPLED RECEPTOR HG38


Mass: 60366.457 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATIONS AT ASN 63,77,208,500 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O75473
#2: Protein R-SPONDIN-1 / ROOF PLATE-SPECIFIC SPONDIN-1 / HRSPO1


Mass: 13706.780 Da / Num. of mol.: 2 / Fragment: FU1FU2, RESIDUES 31-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q2MKA7
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
Sequence detailsN-TERMINAL 6XHISTAG, PLUS ENLYFQGS AND C-TERMINAL AAA INTRODUCED BY CLONING N-TERMINAL GS AND C- ...N-TERMINAL 6XHISTAG, PLUS ENLYFQGS AND C-TERMINAL AAA INTRODUCED BY CLONING N-TERMINAL GS AND C-TERMINAL AAA ADDED BY CLONING PLASMID, PLUS C-TERMINAL 6XHIS TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.31→48.3 Å / Num. obs: 19429 / % possible obs: 99.2 % / Observed criterion σ(I): 2.3 / Redundancy: 7.4 % / Biso Wilson estimate: 177.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.4

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 4.3→48.171 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
Details: EXTENDED C-TERMINAL REGION MODELLED WITH ZERO OCCUPANCY
RfactorNum. reflection% reflection
Rfree0.2679 990 5.1 %
Rwork0.243 --
obs0.2442 19366 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 213.4 Å2
Refinement stepCycle: LAST / Resolution: 4.3→48.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8738 0 95 0 8833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089057
X-RAY DIFFRACTIONf_angle_d1.54312275
X-RAY DIFFRACTIONf_dihedral_angle_d16.8693342
X-RAY DIFFRACTIONf_chiral_restr0.0621432
X-RAY DIFFRACTIONf_plane_restr0.0081576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3002-4.52670.3781380.30632521X-RAY DIFFRACTION98
4.5267-4.81010.2941440.24492513X-RAY DIFFRACTION99
4.8101-5.18110.24911640.21122547X-RAY DIFFRACTION100
5.1811-5.70180.28791360.1952608X-RAY DIFFRACTION100
5.7018-6.52510.26071450.21822611X-RAY DIFFRACTION100
6.5251-8.21430.29131300.25152691X-RAY DIFFRACTION100
8.2143-48.17440.23911330.2552885X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 41.6137 Å / Origin y: -12.4197 Å / Origin z: 25.3993 Å
111213212223313233
T1.1459 Å2-0.1747 Å2-0.017 Å2-1.4865 Å2-0.1295 Å2--1.1699 Å2
L2.0067 °2-0.4147 °20.5369 °2-0.2924 °2-0.1799 °2--0.425 °2
S-0.3162 Å °0.4512 Å °-0.1909 Å °0.0495 Å °0.1934 Å °-0.0254 Å °-0.0968 Å °0.0575 Å °0.1359 Å °
Refinement TLS groupSelection details: ALL

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