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- PDB-4ufs: Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the... -

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Basic information

Entry
Database: PDB / ID: 4ufs
TitleLow resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5 and ZNRF3
Components
  • E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
  • LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
  • R-SPONDIN-2
KeywordsSIGNALING PROTEIN / WNT / LGR / RSPO
Function / homology
Function and homology information


trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / protein-hormone receptor activity / Regulation of FZD by ubiquitination ...trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / protein-hormone receptor activity / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / G protein-coupled peptide receptor activity / frizzled binding / embryonic forelimb morphogenesis / regulation of canonical Wnt signaling pathway / embryonic hindlimb morphogenesis / limb development / epithelial tube branching involved in lung morphogenesis / negative regulation of Wnt signaling pathway / bone mineralization / plasma membrane => GO:0005886 / inner ear development / hair follicle development / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / trans-Golgi network membrane / stem cell proliferation / G protein-coupled receptor activity / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / osteoblast differentiation / ubiquitin-protein transferase activity / transmembrane signaling receptor activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / heparin binding / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / protein ubiquitination / G protein-coupled receptor signaling pathway / signaling receptor binding / Golgi apparatus / cell surface / extracellular region / nucleoplasm / metal ion binding / plasma membrane
Similarity search - Function
E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / Spondin-like TSP1 domain / Spondin-like TSP1 domain / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Leucine rich repeat N-terminal domain / Ring finger domain ...E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / Spondin-like TSP1 domain / Spondin-like TSP1 domain / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Leucine rich repeat N-terminal domain / Ring finger 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. / Ring finger / Growth factor receptor cysteine-rich domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Leucine-rich repeat-containing G-protein coupled receptor 5 / E3 ubiquitin-protein ligase ZNRF3 / R-spondin-2 / E3 ubiquitin-protein ligase ZNRF3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.8 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal Structure of R-Spondin 2 in Complex with the Ectodomains of its Receptors Lgr5 and Znrf3.
Authors: Zebisch, M. / Yvonne Jones, E.
History
DepositionMar 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Structure summary
Revision 1.2Aug 12, 2015Group: Database references
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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: R-SPONDIN-2
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3


Theoretical massNumber of molelcules
Total (without water)86,2593
Polymers86,2593
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-9.2 kcal/mol
Surface area42010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)188.609, 188.609, 165.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 / G-PROTEIN COUPLED RECEPTOR 49 / G-PROTEIN COUPLED RECEPTOR 6 7 / G-PROTEIN COUPLED RECEPTOR HG38 / LGR5


Mass: 54108.453 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544
Source method: isolated from a genetically manipulated source
Details: UNSTRUCTURED LOOP REPLACED WITH SHORT LINKER, A488-H537 TO NGNNGD
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: O75473
#2: Protein R-SPONDIN-2 / CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2 / CRISTIN-2 / MCRISTIN-2 / ROOF ...CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2 / CRISTIN-2 / MCRISTIN-2 / ROOF PLATE-SPECIFIC SPONDIN-2 / RSPO2


Mass: 13946.869 Da / Num. of mol.: 1 / Fragment: FU1-FU2, RESIDUES 39-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BFU0
#3: Protein E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 / ZINC/RING FINGER PROTEIN 3 / ZNRF3


Mass: 18203.557 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 53-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: Q5SSZ7, UniProt: Q9ULT6*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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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: 4.61 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 6
Details: 0.100 M AMMONIUM ACETATE, 0.600 M SODIUM CHLORIDE, 0.050 M MES PH 6.0, 0.005 M MAGNESIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.8→40 Å / Num. obs: 7509 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 212 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.5
Reflection shellResolution: 4.8→5.37 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 4.8→133.37 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / ESU R Free: 1.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROSMART RESTRAINTS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.31262 393 5.2 %RANDOM
Rwork0.26986 ---
obs0.27215 7115 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 256.386 Å2
Baniso -1Baniso -2Baniso -3
1-7.39 Å2-0 Å20 Å2
2--7.39 Å20 Å2
3----14.77 Å2
Refinement stepCycle: LAST / Resolution: 4.8→133.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5582 0 0 0 5582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195713
X-RAY DIFFRACTIONr_bond_other_d00.025437
X-RAY DIFFRACTIONr_angle_refined_deg0.8481.9727756
X-RAY DIFFRACTIONr_angle_other_deg3.66312523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7575712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64224.297256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48215973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2961533
X-RAY DIFFRACTIONr_chiral_restr0.0510.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021311
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_it21.2124.6572860
X-RAY DIFFRACTIONr_mcbond_other21.21224.6562859
X-RAY DIFFRACTIONr_mcangle_it33.74536.9243568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it20.93426.6412852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 4.8→4.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 27 -
Rwork0.373 531 -
obs--99.82 %

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