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- PDB-4c9r: Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 cr... -

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Basic information

Entry
Database: PDB / ID: 4c9r
TitleXenopus ZNRF3 ectodomain in complex with Xenopus 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


anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / dorsal/ventral axis specification / lysosomal protein catabolic process ...anal fin development / caudal fin development / dorsal fin development / pectoral fin development / pelvic fin development / Regulation of FZD by ubiquitination / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / dorsal/ventral axis specification / lysosomal protein catabolic process / BMP receptor binding / limb development / anterior/posterior pattern specification / 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 / ubiquitin protein ligase activity / heparin binding / ubiquitin-dependent protein catabolic process / lysosome / protein ubiquitination / extracellular space / 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 speciesXENOPUS TROPICALIS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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


Theoretical massNumber of molelcules
Total (without water)68,5524
Polymers68,5524
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-15.3 kcal/mol
Surface area28570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.990, 81.229, 71.632
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20494.014 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 24-191
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: Q08D68, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein R-SPONDIN-2 / ROOF PLATE-SPECIFIC SPONDIN-2 / RSPO2


Mass: 13781.749 Da / Num. of mol.: 2 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.77 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.1→66 Å / Num. obs: 32344 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 17 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.1

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Processing

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

Resolution: 2.1→65.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.748 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24608 1128 3.5 %RANDOM
Rwork0.18794 ---
obs0.19 31015 93.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.77 Å2
2--3.02 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 0 220 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194242
X-RAY DIFFRACTIONr_bond_other_d0.0010.024000
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9725721
X-RAY DIFFRACTIONr_angle_other_deg0.83.0089203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77524200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3315748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5311535
X-RAY DIFFRACTIONr_chiral_restr0.0920.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02955
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 40 -
Rwork0.305 1325 -
obs--53.89 %

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