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- PDB-4c99: Mouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crysta... -

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Basic information

Entry
Database: PDB / ID: 4c99
TitleMouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crystal form I
Components
  • E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
  • R-SPONDIN-2
KeywordsLIGASE/SIGNALING PROTEIN / LIGASE-SIGNALING PROTEIN COMPLEX / WNT / RNF43 / LGR4 / LGR5 / LGR6 / RSPO / R-SPONDIN / R-SPO / RSPO1 / RSPO3 / RSPO4 / RECEPTOR / MEMBRANE / SIGNALLING
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 / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / frizzled binding / embryonic forelimb morphogenesis ...trachea cartilage morphogenesis / negative regulation of odontogenesis of dentin-containing tooth / lung growth / regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / dopaminergic neuron differentiation / frizzled binding / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / regulation of canonical Wnt signaling pathway / limb development / epithelial tube branching involved in lung morphogenesis / bone mineralization / negative regulation of Wnt signaling pathway / canonical Wnt signaling pathway / stem cell proliferation / negative regulation of canonical Wnt signaling pathway / RING-type E3 ubiquitin transferase / Wnt signaling pathway / ubiquitin-protein transferase activity / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / heparin binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / signaling receptor binding / cell surface / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
Spondin-like TSP1 domain / Spondin-like TSP1 domain / E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / : / R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 ...Spondin-like TSP1 domain / Spondin-like TSP1 domain / E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / : / R-spondin, Fu-CRD domain / : / Furin-like repeat, cysteine-rich / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Glucose Oxidase; domain 1 - #30 / Ring finger domain / Glucose Oxidase; domain 1 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Furin-like repeat / Furin-like repeats / Ring finger / Growth factor receptor cysteine-rich domain superfamily / 3-Layer(bba) Sandwich / Zinc finger RING-type profile. / Zinc finger, RING-type / Ribbon / Zinc finger, RING/FYVE/PHD-type / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ZNRF3 / R-spondin-2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: Nat.Commun. / Year: 2013
Title: Structural and Molecular Basis of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition by the Wnt Agonist R-Spondin.
Authors: Zebisch, M. / Xu, Y. / Krastev, C. / Macdonald, B.T. / Chen, M. / Gilbert, R.J.C. / He, X. / Jones, E.Y.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. 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: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
B: R-SPONDIN-2
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
D: R-SPONDIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7595
Polymers64,7234
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-20.8 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.800, 77.206, 130.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, 0.042, -0.053), (-0.044, -0.998, 0.039), (-0.052, 0.041, 0.998)
Vector: 4.315, 0.488, -0.141)

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 / ZINC/RING FINGER PROTEIN 3 / ZNRF3


Mass: 18203.557 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 53-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: Q5SSZ7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein R-SPONDIN-2 / CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PR


Mass: 14158.086 Da / Num. of mol.: 2 / Fragment: FU1-FU2, RESIDUES 37-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BFU0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.19 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→66 Å / Num. obs: 15525 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 71.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→66.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.875 / SU B: 21.184 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32285 772 5 %RANDOM
Rwork0.23616 ---
obs0.2405 14706 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.796 Å2
Baniso -1Baniso -2Baniso -3
1--5.19 Å20 Å20 Å2
2--5 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→66.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 1 0 3968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194061
X-RAY DIFFRACTIONr_bond_other_d0.0010.023784
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9625482
X-RAY DIFFRACTIONr_angle_other_deg0.8253.0088692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7045510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42323.99193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36415694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2091531
X-RAY DIFFRACTIONr_chiral_restr0.0880.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 68 -
Rwork0.31 1059 -
obs--99.91 %

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