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- PDB-4c8f: mouse ZNRF3 ectodomain crystal form IV -

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Basic information

Entry
Database: PDB / ID: 4c8f
Titlemouse ZNRF3 ectodomain crystal form IV
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: 2.69 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
DepositionSep 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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 "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
D: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3


Theoretical massNumber of molelcules
Total (without water)72,8144
Polymers72,8144
Non-polymers00
Water00
1
A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
D: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3


Theoretical massNumber of molelcules
Total (without water)36,4072
Polymers36,4072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-10.9 kcal/mol
Surface area13920 Å2
MethodPISA
2
B: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
C: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3


Theoretical massNumber of molelcules
Total (without water)36,4072
Polymers36,4072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-9.5 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.198, 112.629, 62.220
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number5
Space group name H-MC121

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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.: 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)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 % / 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: Jan 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.7→49 Å / Num. obs: 18914 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8

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Processing

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

Resolution: 2.69→41.43 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.827 / SU B: 16.034 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R: 1.588 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.34053 922 5 %RANDOM
Rwork0.23472 ---
obs0.23995 17441 87.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å26.76 Å2
2---2.74 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.69→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 0 0 4174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194242
X-RAY DIFFRACTIONr_bond_other_d0.0010.024170
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9685742
X-RAY DIFFRACTIONr_angle_other_deg0.80139582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9145541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60624.343175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.43515731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7641528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
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: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 45 -
Rwork0.263 793 -
obs--54.88 %

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