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- PDB-5un6: Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset -

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Basic information

Entry
Database: PDB / ID: 5un6
TitleFrizzled-8 complex with designed surrogate Wnt agonist, A1 dataset
Components
  • Designed Wnt agonist B12
  • Frizzled-8
KeywordsSIGNALING PROTEIN/DE NOVO 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: 3.2 Å
AuthorsJanda, C.Y. / Garcia, K.C. / Jude, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097015 United States
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 / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high
Revision 1.6Nov 20, 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
A: Frizzled-8
E: Designed Wnt agonist B12
F: Designed Wnt agonist B12
G: Designed Wnt agonist B12
H: Designed Wnt agonist B12
B: Frizzled-8
C: Frizzled-8
D: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)115,1448
Polymers115,1448
Non-polymers00
Water00
1
A: Frizzled-8
E: Designed Wnt agonist B12


Theoretical massNumber of molelcules
Total (without water)28,7862
Polymers28,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-12 kcal/mol
Surface area12750 Å2
MethodPISA
2
F: Designed Wnt agonist B12
B: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)28,7862
Polymers28,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area12620 Å2
MethodPISA
3
G: Designed Wnt agonist B12
C: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)28,7862
Polymers28,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area12350 Å2
MethodPISA
4
H: Designed Wnt agonist B12
D: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)28,7862
Polymers28,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.420, 36.450, 125.530
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Frizzled-8 / hFz8


Mass: 14961.150 Da / Num. of mol.: 4 / Fragment: UNP residues 28-150 / Mutation: Q22N
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.: 4
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
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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% PEG 3000, 0.1 M Sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Details: the diffraction images at the SBGrid databank. DOI is 10.15785/SBGRID/422
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→38.76 Å / Num. obs: 17882 / % possible obs: 99.81 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rsym value: 0.115 / Net I/σ(I): 12.88
Reflection shellResolution: 3.2→3.418 Å / Num. unique obs: 800 / CC1/2: 0.829 / Rsym value: 0.601 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSMarch 30, 2013data reduction
XSCALEJune 17, 2015data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0A, calculated model of B12

4f0a


Resolution: 3.2→19.816 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.2475 1644 9.19 %
Rwork0.2002 --
obs0.2047 17882 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 0 0 6291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036436
X-RAY DIFFRACTIONf_angle_d0.6328726
X-RAY DIFFRACTIONf_dihedral_angle_d10.8033960
X-RAY DIFFRACTIONf_chiral_restr0.04976
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.29390.32471220.26511366X-RAY DIFFRACTION99
3.2939-3.39970.3141380.25511311X-RAY DIFFRACTION100
3.3997-3.52050.32011340.25471331X-RAY DIFFRACTION99
3.5205-3.66060.2741400.23151334X-RAY DIFFRACTION98
3.6606-3.82610.27631420.21821306X-RAY DIFFRACTION99
3.8261-4.02620.24141260.21291384X-RAY DIFFRACTION99
4.0262-4.27610.2291320.18691308X-RAY DIFFRACTION100
4.2761-4.60250.23911390.17311381X-RAY DIFFRACTION100
4.6025-5.05860.22651410.17951355X-RAY DIFFRACTION100
5.0586-5.77470.24341330.19541355X-RAY DIFFRACTION99
5.7747-7.21660.27651480.20981398X-RAY DIFFRACTION99
7.2166-19.81640.21490.17031409X-RAY DIFFRACTION98

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