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- PDB-4c9e: Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Sel... -

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Basic information

Entry
Database: PDB / ID: 4c9e
TitleMouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II
Components
  • E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
  • R-SPONDIN-2
KeywordsLIGASE/SIGNALING PROTEIN / LIGASE-SIGNALING PROTEIN COMPLEX / WNT / RNF43 / LGR4 / LGR5 / LGR6 / RSPO / R-SPO / RSPO1 / RSPO3 / RSPO4 / RECEPTOR / MEMBRANE / SIGNALLING
Function / homology
Function and homology information


anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / 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 ...anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / 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 / lysosomal protein catabolic process / dorsal/ventral axis specification / BMP receptor binding / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of Wnt signaling pathway / negative regulation of BMP signaling pathway / BMP signaling pathway / stem cell proliferation / skeletal system development / negative regulation of canonical Wnt signaling pathway / RING-type E3 ubiquitin transferase / Wnt signaling pathway / ubiquitin-protein transferase activity / heparin binding / ubiquitin-dependent protein catabolic process / lysosome / protein ubiquitination / extracellular space / 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 / : / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 ...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 / : / 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 / Growth factor receptor cysteine-rich domain superfamily / Ring finger / 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
R-spondin-2 / E3 ubiquitin-protein ligase ZNRF3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
XENOPUS TROPICALIS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 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 6, 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_conn / struct_sheet
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_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
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. THE SHEETS PRESENTED AS "EA" 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 "GA" 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
E: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
F: R-SPONDIN-2
G: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
H: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)128,1298
Polymers128,1298
Non-polymers00
Water00
1
A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
B: R-SPONDIN-2
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
D: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)64,0644
Polymers64,0644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-27.1 kcal/mol
Surface area30560 Å2
MethodPQS
2
E: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
F: R-SPONDIN-2
G: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
H: R-SPONDIN-2


Theoretical massNumber of molelcules
Total (without water)64,0644
Polymers64,0644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-19.3 kcal/mol
Surface area30060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.991, 71.279, 72.109
Angle α, β, γ (deg.)69.29, 61.48, 84.31
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 18203.557 Da / Num. of mol.: 4 / 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 / RSPO2 / ROOF PLATE-SPECIFIC SPONDIN-2


Mass: 13828.644 Da / Num. of mol.: 4 / Fragment: FU1-FU2, RESIDUES 35-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog)
Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q5M7L6
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: 47.28 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3→35.34 Å / Num. obs: 22849 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.4

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Processing

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

Resolution: 3→35.37 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.853 / SU B: 27.665 / SU ML: 0.518 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.33378 1178 5.2 %RANDOM
Rwork0.24523 ---
obs0.24977 21538 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.366 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å2-4.04 Å21.85 Å2
2---0.83 Å21.82 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 3→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7644 0 0 0 7644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197821
X-RAY DIFFRACTIONr_bond_other_d0.0010.027308
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.97410589
X-RAY DIFFRACTIONr_angle_other_deg0.8053.00916734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63551016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50623.673324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.122151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4091558
X-RAY DIFFRACTIONr_chiral_restr0.0740.21154
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021742
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 78 -
Rwork0.28 1504 -
obs--92.79 %

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