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- PDB-4c8p: mouse ZNRF3 ectodomain crystal form V, disulfide-bridged S90C variant -

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Basic information

Entry
Database: PDB / ID: 4c8p
Titlemouse ZNRF3 ectodomain crystal form V, disulfide-bridged S90C variant
ComponentsE3 UBIQUITIN-PROTEIN LIGASE ZNRF3
KeywordsLIGASE / WNT / RNF43 / LGR4 / LGR5 / LGR6 / RSPO / R-SPONDIN / R-SPO / RSPO1 / RSPO2 / RSPO3 / RSPO4 / RECEPTOR / MEMBRANE / SIGNALLING
Function / homology
Function and homology information


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 / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of Wnt signaling pathway / stem cell proliferation / negative regulation of canonical Wnt signaling pathway ...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 / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of 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 / ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / plasma membrane
Similarity search - Function
E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / : / Glucose Oxidase; domain 1 - #30 / Ring finger domain / Glucose Oxidase; domain 1 / Ring finger / 3-Layer(bba) Sandwich / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / : / Glucose Oxidase; domain 1 - #30 / Ring finger domain / Glucose Oxidase; domain 1 / Ring finger / 3-Layer(bba) Sandwich / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ZNRF3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
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 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Oct 16, 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.

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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


Theoretical massNumber of molelcules
Total (without water)18,2201
Polymers18,2201
Non-polymers00
Water37821
1
A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3

A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3


Theoretical massNumber of molelcules
Total (without water)36,4392
Polymers36,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area2220 Å2
ΔGint-7.4 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.725, 74.297, 38.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 18219.621 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 53-205 / Mutation: YES
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.32 Å3/Da / Density % sol: 47.09 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→46 Å / Num. obs: 10421 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5

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Processing

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

Resolution: 2.1→46.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.836 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28562 481 4.9 %RANDOM
Rwork0.20406 ---
obs0.20766 9382 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.738 Å2
Baniso -1Baniso -2Baniso -3
1--6.41 Å20 Å2-0 Å2
2---4.97 Å2-0 Å2
3---11.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 0 21 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191130
X-RAY DIFFRACTIONr_bond_other_d0.0010.021113
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9751530
X-RAY DIFFRACTIONr_angle_other_deg0.8473.0022562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29124.46847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29815198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.158157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
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→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 29 -
Rwork0.355 581 -
obs--79.84 %

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