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- PDB-5un5: Frizzled-8 complex with designed surrogate Wnt agonist, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5un5
TitleFrizzled-8 complex with designed surrogate Wnt agonist, crystal form 1
Components
  • Designed Wnt agonist B12
  • Frizzled-8
KeywordsSIGNALING PROTEIN/De Novo Protein / SIGNALING PROTEIN / SIGNALING PROTEIN-De Novo Protein complex
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Signaling by RNF43 mutants / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / neuronal dense core vesicle / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / PDZ domain binding ...Wnt-Frizzled-LRP5/6 complex / Signaling by RNF43 mutants / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / neuronal dense core vesicle / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / PDZ domain binding / Asymmetric localization of PCP proteins / G protein-coupled receptor activity / neuron differentiation / T cell differentiation in thymus / angiogenesis / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Frizzled 8, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily ...Frizzled 8, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsJanda, C.Y. / Garcia, K.C.
CitationJournal: Nature / Year: 2017
Title: Surrogate Wnt agonists that phenocopy canonical Wnt and beta-catenin signalling.
Authors: Janda, C.Y. / Dang, L.T. / You, C. / Chang, J. / de Lau, W. / Zhong, Z.A. / Yan, K.S. / Marecic, O. / Siepe, D. / Li, X. / Moody, J.D. / Williams, B.O. / Clevers, H. / Piehler, J. / Baker, D. ...Authors: Janda, C.Y. / Dang, L.T. / You, C. / Chang, J. / de Lau, W. / Zhong, Z.A. / Yan, K.S. / Marecic, O. / Siepe, D. / Li, X. / Moody, J.D. / Williams, B.O. / Clevers, H. / Piehler, J. / Baker, D. / Kuo, C.J. / Garcia, K.C.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Frizzled-8
A: Frizzled-8
D: Designed Wnt agonist B12
C: Designed Wnt agonist B12


Theoretical massNumber of molelcules
Total (without water)57,5724
Polymers57,5724
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-67 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.200, 77.510, 81.430
Angle α, β, γ (deg.)90.00, 92.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Frizzled-8 / hFz8


Mass: 14961.150 Da / Num. of mol.: 2 / Fragment: UNP residues 28-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H461
#2: Protein Designed Wnt agonist B12


Mass: 13824.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 42-49% PEG 400, 0.1 M Tris pH 7.8-8.2, 0.2 M NaCl / PH range: 7.8-8.2

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Data collection

DiffractionMean temperature: 100 K
Details: the diffraction images at the SBGrid databank, DOI is 10.15785/SBGRID/423
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→41.1523 Å / Num. obs: 10346 / % possible obs: 99.1 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rsym value: 0.119 / Net I/σ(I): 11.5
Reflection shellResolution: 2.98→3.05 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 679 / CC1/2: 0.577 / Rsym value: 1.267 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSMarch 30, 2013data reduction
XSCALE2015-08-21data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0A

4f0a


Resolution: 2.994→41.152 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1036 10.02 %
Rwork0.2253 --
obs0.2278 10335 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.994→41.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 0 4 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023302
X-RAY DIFFRACTIONf_angle_d0.5334466
X-RAY DIFFRACTIONf_dihedral_angle_d7.8642044
X-RAY DIFFRACTIONf_chiral_restr0.036491
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9943-3.15210.33861450.32911263X-RAY DIFFRACTION94
3.1521-3.34950.34261410.29021316X-RAY DIFFRACTION100
3.3495-3.6080.30711520.25781332X-RAY DIFFRACTION100
3.608-3.97080.28581480.2371323X-RAY DIFFRACTION100
3.9708-4.54480.21081440.19891363X-RAY DIFFRACTION100
4.5448-5.72350.23381500.21311328X-RAY DIFFRACTION100
5.7235-41.15620.21381560.19851374X-RAY DIFFRACTION100

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