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- PDB-8x0t: Frizzled8 CRD in complex with pF8_AC3 Fab -

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Basic information

Entry
Database: PDB / ID: 8x0t
TitleFrizzled8 CRD in complex with pF8_AC3 Fab
Components
  • Frizzled-8
  • pF8_AC3 Heavy chain
  • pF8_AC3 Light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Antigen-antibody complex / cell signaling / SIGNALING PROTEIN-IMMUNE SYSTEM 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 / Asymmetric localization of PCP proteins ...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 / Asymmetric localization of PCP proteins / PDZ domain binding / 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/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. ...Frizzled 8, 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.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, N. / Ge, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0902700 China
CitationJournal: Int J Biol Macromol / Year: 2023
Title: Identification and functional validation of FZD8-specific antibodies.
Authors: Li, N. / Ge, Q. / Guo, Q. / Tao, Y.
History
DepositionNov 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Frizzled-8
H: pF8_AC3 Heavy chain
L: pF8_AC3 Light chain


Theoretical massNumber of molelcules
Total (without water)63,2533
Polymers63,2533
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-42 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.701, 76.149, 220.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Frizzled-8 / Fz-8 / hFz8


Mass: 15237.465 Da / Num. of mol.: 1 / Mutation: N49Q
Source method: isolated from a genetically manipulated source
Details: FZD8 CRD domain with N49Q point mutation and C-terminal 6xHis tag
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD8 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9H461
#2: Antibody pF8_AC3 Heavy chain


Mass: 25270.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody pF8_AC3 Light chain


Mass: 22745.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 32% PEG4000, 0.1 M Tris, pH 8.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→46.88 Å / Num. obs: 21022 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 47.67 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1367 / Rpim(I) all: 0.0391 / Rrim(I) all: 0.1423 / Net I/σ(I): 14.99
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.169 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2074 / CC1/2: 0.867 / CC star: 0.964 / Rpim(I) all: 0.3372 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.88 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 1050 5 %0
Rwork0.238 ---
obs0.2397 20991 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 0 37 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034353
X-RAY DIFFRACTIONf_angle_d0.7125935
X-RAY DIFFRACTIONf_dihedral_angle_d16.8951568
X-RAY DIFFRACTIONf_chiral_restr0.046646
X-RAY DIFFRACTIONf_plane_restr0.007770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.40011340.32522459X-RAY DIFFRACTION100
2.61-2.750.42451260.32242455X-RAY DIFFRACTION100
2.75-2.920.37451280.30442451X-RAY DIFFRACTION100
2.92-3.150.37031390.29872446X-RAY DIFFRACTION100
3.15-3.470.29561160.26422509X-RAY DIFFRACTION100
3.47-3.970.28071490.22652475X-RAY DIFFRACTION100
3.97-50.21581210.18572514X-RAY DIFFRACTION100
5-46.880.25841380.20632633X-RAY DIFFRACTION100

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