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- PDB-7x8q: Frizzled-10 CRD in complex with F10_A9 Fab -

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Basic information

Entry
Database: PDB / ID: 7x8q
TitleFrizzled-10 CRD in complex with F10_A9 Fab
Components
  • Antibody F10_A9 Fab, Heavy chain
  • Antibody F10_A9 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 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 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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 1.0Jan 18, 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

Downloads & links

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Assembly

Deposited unit
A: Frizzled-10
B: Antibody F10_A9 Fab, Light chain
C: Antibody F10_A9 Fab, Heavy chain
D: Frizzled-10
E: Antibody F10_A9 Fab, Light chain
F: Antibody F10_A9 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)125,5946
Polymers125,5946
Non-polymers00
Water3,189177
1
A: Frizzled-10
B: Antibody F10_A9 Fab, Light chain
C: Antibody F10_A9 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,7973
Polymers62,7973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-34 kcal/mol
Surface area25370 Å2
MethodPISA
2
D: Frizzled-10
E: Antibody F10_A9 Fab, Light chain
F: Antibody F10_A9 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,7973
Polymers62,7973
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-31 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.452, 156.452, 94.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

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Components

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


Mass: 14903.371 Da / Num. of mol.: 2 / 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 F10_A9 Fab, Light chain


Mass: 23231.803 Da / Num. of mol.: 2
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 Antibody F10_A9 Fab, Heavy chain


Mass: 24661.635 Da / Num. of mol.: 2
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.: 177 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.0, 30% Jeffamine ED-2001, pH 7.0

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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 PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→36.88 Å / Num. obs: 34538 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 41.22 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.026 / Rrim(I) all: 0.108 / Χ2: 0.961 / Net I/σ(I): 29.2
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 3.75 / Num. unique obs: 1698 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.217 / Rrim(I) all: 0.905 / Χ2: 0.926 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CM4

5cm4


Resolution: 2.65→36.88 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1653 4.83 %
Rwork0.2051 32573 -
obs0.2071 34226 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.48 Å2 / Biso mean: 50.221 Å2 / Biso min: 19.23 Å2
Refinement stepCycle: final / Resolution: 2.65→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8270 0 0 177 8447
Biso mean---37.83 -
Num. residues----1080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.730.29271240.252618274298
2.73-2.820.25151150.24942700281599
2.82-2.920.31121350.25762660279599
2.92-3.030.34191490.26292665281499
3.03-3.170.33891440.250726732817100
3.17-3.340.27861490.225226922841100
3.34-3.550.26691370.224827092846100
3.55-3.820.24631450.208627042849100
3.82-4.210.23461330.187827292862100
4.21-4.810.17921430.158927612904100
4.81-6.060.21761490.178827802929100
6.06-36.880.2191300.1842882301298

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