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- PDB-7x8t: Frizzled 10 CRD in complex with hB9L9.3 Fab -

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Basic information

Entry
Database: PDB / ID: 7x8t
TitleFrizzled 10 CRD in complex with hB9L9.3 Fab
Components
  • Antibody hB9L9.3 Fab, Heavy chain
  • Antibody hB9L9.3 Fab, Light chain
  • Frizzled-10
KeywordsSIGNALING PROTEIN / Antibody
Function / homology
Function and homology information


Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / canonical Wnt signaling pathway / cellular response to retinoic acid / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / G protein-coupled receptor activity / neuron differentiation ...Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / canonical Wnt signaling pathway / cellular response to retinoic acid / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / G protein-coupled receptor activity / neuron differentiation / cell surface / extracellular space / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
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 ...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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsGe, Q. / Wang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770895 China
CitationJournal: Structure / Year: 2023
Title: An epitope-directed selection strategy facilitating the identification of Frizzled receptor selective antibodies.
Authors: Ge, Q. / Teng, M. / Li, X. / Guo, Q. / Tao, Y.
History
DepositionMar 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 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-10
B: Antibody hB9L9.3 Fab, Light chain
C: Antibody hB9L9.3 Fab, Heavy chain
D: Frizzled-10
E: Antibody hB9L9.3 Fab, Light chain
F: Antibody hB9L9.3 Fab, Heavy chain
G: Frizzled-10
H: Antibody hB9L9.3 Fab, Light chain
I: Antibody hB9L9.3 Fab, Heavy chain
J: Frizzled-10
K: Antibody hB9L9.3 Fab, Light chain
L: Antibody hB9L9.3 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)249,21912
Polymers249,21912
Non-polymers00
Water20,6091144
1
A: Frizzled-10
B: Antibody hB9L9.3 Fab, Light chain
C: Antibody hB9L9.3 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,3053
Polymers62,3053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-27 kcal/mol
Surface area25210 Å2
MethodPISA
2
D: Frizzled-10
E: Antibody hB9L9.3 Fab, Light chain
F: Antibody hB9L9.3 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,3053
Polymers62,3053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-26 kcal/mol
Surface area25050 Å2
MethodPISA
3
G: Frizzled-10
H: Antibody hB9L9.3 Fab, Light chain
I: Antibody hB9L9.3 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,3053
Polymers62,3053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-27 kcal/mol
Surface area24910 Å2
MethodPISA
4
J: Frizzled-10
K: Antibody hB9L9.3 Fab, Light chain
L: Antibody hB9L9.3 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,3053
Polymers62,3053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.456, 100.794, 99.149
Angle α, β, γ (deg.)110.074, 89.935, 113.793
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Frizzled-10 / Fz-10 / hFz10 / FzE7


Mass: 14903.371 Da / Num. of mol.: 4 / Mutation: N48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD10 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9ULW2
#2: Antibody
Antibody hB9L9.3 Fab, Light chain


Mass: 22381.525 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody
Antibody hB9L9.3 Fab, Heavy chain


Mass: 25019.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Na citrate, pH 5.0, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 83801 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.49 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.068 / Rrim(I) all: 0.128 / Χ2: 0.829 / Net I/σ(I): 5.3 / Num. measured all: 290369
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.30.34541630.8950.2270.4150.88598
2.54-2.593.40.31941890.9190.2020.3790.8998.1
2.59-2.643.60.29241190.9420.1790.3430.90898.2
2.64-2.693.60.25341830.9570.1550.2970.89698.2
2.69-2.753.60.23841590.9620.1460.280.86598.2
2.75-2.823.50.21842010.9590.1350.2570.87898.2
2.82-2.893.50.1941700.9640.1180.2240.85798.4
2.89-2.963.50.17641670.9680.1090.2070.88498.6
2.96-3.053.50.15841690.9720.0980.1870.86498.7
3.05-3.153.30.13742020.9750.0890.1640.8598.7
3.15-3.263.30.11842100.9790.0780.1430.87298.8
3.26-3.393.30.10841930.9820.070.1290.8898.8
3.39-3.553.70.10241670.9860.0620.120.85499
3.55-3.733.60.09842090.9830.060.1150.90499.1
3.73-3.973.60.08442370.9860.0520.0990.80799.2
3.97-4.273.50.07741930.9860.0480.0910.78499.2
4.27-4.73.20.0742320.9850.0470.0840.75899.4
4.7-5.383.40.07442050.9860.0470.0880.7699.5
5.38-6.783.60.07642260.9870.0450.0890.62499.6
6.78-503.40.05842070.9910.0370.0680.55199.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CM4

5cm4


Resolution: 2.51→46.06 Å / SU ML: 0.2647 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.5754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 4116 4.93 %0
Rwork0.1758 79454 --
obs0.1777 83570 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 2.51→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16492 0 0 1144 17636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012116912
X-RAY DIFFRACTIONf_angle_d1.293123028
X-RAY DIFFRACTIONf_chiral_restr0.07442516
X-RAY DIFFRACTIONf_plane_restr0.00843000
X-RAY DIFFRACTIONf_dihedral_angle_d14.42386092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.530.2811230.232396X-RAY DIFFRACTION86.33
2.53-2.570.27831380.22562743X-RAY DIFFRACTION97.93
2.57-2.60.28521440.22222794X-RAY DIFFRACTION97.97
2.6-2.630.28181570.20992632X-RAY DIFFRACTION98.1
2.63-2.670.26481340.21172790X-RAY DIFFRACTION97.99
2.67-2.710.26371590.21652686X-RAY DIFFRACTION98
2.71-2.750.24451420.21782774X-RAY DIFFRACTION98.18
2.75-2.790.29791520.21982730X-RAY DIFFRACTION97.96
2.79-2.840.26131220.21092768X-RAY DIFFRACTION98.3
2.84-2.880.26851360.19872754X-RAY DIFFRACTION98.43
2.88-2.940.25651330.20332719X-RAY DIFFRACTION98.38
2.94-2.990.25911310.20272783X-RAY DIFFRACTION98.68
2.99-3.050.26361380.20382770X-RAY DIFFRACTION98.71
3.05-3.120.27931610.20972793X-RAY DIFFRACTION98.7
3.12-3.190.29541420.20512714X-RAY DIFFRACTION98.72
3.19-3.270.23361540.19582765X-RAY DIFFRACTION98.61
3.27-3.360.22451460.17872736X-RAY DIFFRACTION98.63
3.36-3.460.23261630.17132744X-RAY DIFFRACTION98.94
3.46-3.570.22291300.17122793X-RAY DIFFRACTION98.85
3.57-3.70.20711440.17072747X-RAY DIFFRACTION99.11
3.7-3.850.19431470.17262752X-RAY DIFFRACTION99.01
3.85-4.020.16841340.15352808X-RAY DIFFRACTION99.19
4.02-4.230.17071380.14972745X-RAY DIFFRACTION99.28
4.23-4.50.15281420.13422792X-RAY DIFFRACTION99.12
4.5-4.850.17251710.13522721X-RAY DIFFRACTION99.18
4.85-5.330.16711350.14872794X-RAY DIFFRACTION99.19
5.33-6.10.19081270.15752792X-RAY DIFFRACTION99.56
6.11-7.680.21791520.1772783X-RAY DIFFRACTION99.53
7.69-46.060.16311210.16522636X-RAY DIFFRACTION93.84

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