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- PDB-8g4y: Structure of ZNRF3 ECD bound to peptide MK1-3.6.10 -

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Basic information

Entry
Database: PDB / ID: 8g4y
TitleStructure of ZNRF3 ECD bound to peptide MK1-3.6.10
Components
  • E3 ubiquitin-protein ligase ZNRF3
  • MK1-3.6.10
KeywordsLIGASE / ubiquitin ligase / Wnt signal / cell surface / CKP
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 / frizzled binding / limb development / plasma membrane => GO:0005886 / Regulation of FZD by ubiquitination / stem cell proliferation / RING-type E3 ubiquitin transferase / 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 / frizzled binding / limb development / plasma membrane => GO:0005886 / Regulation of FZD by ubiquitination / stem cell proliferation / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / metal ion binding / plasma membrane
Similarity search - Function
ZNRF-3, ectodomain / ZNRF-3 Ectodomain / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ZNRF3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsHarris, S.F. / Wu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Chem Biol / Year: 2023
Title: Potent and selective binders of the E3 ubiquitin ligase ZNRF3 stimulate Wnt signaling and intestinal organoid growth.
Authors: Kschonsak, Y.T. / Gao, X. / Miller, S.E. / Hwang, S. / Marei, H. / Wu, P. / Li, Y. / Ruiz, K. / Dorighi, K. / Holokai, L. / Perampalam, P. / Tsai, W.K. / Kee, Y.S. / Agard, N.J. / Harris, S. ...Authors: Kschonsak, Y.T. / Gao, X. / Miller, S.E. / Hwang, S. / Marei, H. / Wu, P. / Li, Y. / Ruiz, K. / Dorighi, K. / Holokai, L. / Perampalam, P. / Tsai, W.K. / Kee, Y.S. / Agard, N.J. / Harris, S.F. / Hannoush, R.N. / de Sousa E Melo, F.
History
DepositionFeb 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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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: MK1-3.6.10


Theoretical massNumber of molelcules
Total (without water)24,1622
Polymers24,1622
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.551, 35.226, 48.856
Angle α, β, γ (deg.)90.00, 109.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 ubiquitin-protein ligase ZNRF3 / RING finger protein 203 / RING-type E3 ubiquitin transferase ZNRF3 / Zinc/RING finger protein 3


Mass: 19703.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNRF3, KIAA1133, RNF203 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q9ULT6, RING-type E3 ubiquitin transferase
#2: Protein/peptide MK1-3.6.10


Mass: 4459.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium citrate pH 4.5, 20% PEG 4000 plus silver bullet A5 (Hampton Research)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.036 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.036 Å / Relative weight: 1
ReflectionResolution: 1.41→46.16 Å / Num. obs: 35592 / % possible obs: 97.3 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Rrim(I) all: 0.062 / Χ2: 0.89 / Net I/σ(I): 14.4
Reflection shellResolution: 1.55→1.64 Å / % possible obs: 96.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.748 / Num. measured all: 22697 / Num. unique obs: 4445 / CC1/2: 0.782 / Rpim(I) all: 0.366 / Rrim(I) all: 0.834 / Χ2: 0.72 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→32.02 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 1715 4.82 %
Rwork0.2134 --
obs0.2145 35592 84.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 0 141 1639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.916
X-RAY DIFFRACTIONf_dihedral_angle_d13.252590
X-RAY DIFFRACTIONf_chiral_restr0.087228
X-RAY DIFFRACTIONf_plane_restr0.009279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.4176270.4558632X-RAY DIFFRACTION19
1.45-1.50.428900.37371679X-RAY DIFFRACTION51
1.5-1.550.34711300.31522375X-RAY DIFFRACTION72
1.55-1.620.30181590.27293051X-RAY DIFFRACTION92
1.62-1.690.2721620.24683207X-RAY DIFFRACTION97
1.69-1.780.25481550.23313260X-RAY DIFFRACTION97
1.78-1.890.2771820.22853227X-RAY DIFFRACTION97
1.89-2.040.25621420.23043283X-RAY DIFFRACTION97
2.04-2.240.24112090.20983228X-RAY DIFFRACTION98
2.24-2.560.22981490.21253318X-RAY DIFFRACTION98
2.57-3.230.21621510.21063355X-RAY DIFFRACTION98
3.23-32.020.20941590.18663262X-RAY DIFFRACTION94

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