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- PDB-7x8p: Frizzled 2 CRD in complex with pF7_A5 Fab -

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Basic information

Entry
Database: PDB / ID: 7x8p
TitleFrizzled 2 CRD in complex with pF7_A5 Fab
Components
  • (Antibody pF7_A5 Fab, ...) x 2
  • Frizzled-2
KeywordsSIGNALING PROTEIN / Antibody
Function / homology
Function and homology information


muscular septum morphogenesis / cochlea morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / hard palate development / Wnt receptor activity / non-canonical Wnt signaling pathway / membranous septum morphogenesis / inner ear receptor cell development / Wnt-protein binding / endothelial cell differentiation ...muscular septum morphogenesis / cochlea morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / hard palate development / Wnt receptor activity / non-canonical Wnt signaling pathway / membranous septum morphogenesis / inner ear receptor cell development / Wnt-protein binding / endothelial cell differentiation / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / outflow tract morphogenesis / canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / TCF dependent signaling in response to WNT / PDZ domain binding / Asymmetric localization of PCP proteins / clathrin-coated endocytic vesicle membrane / G protein-coupled receptor activity / Wnt signaling pathway / neuron differentiation / sensory perception of smell / cell-cell signaling / Ca2+ pathway / focal adhesion / positive regulation of DNA-templated transcription / plasma membrane / cytoplasm
Similarity search - Function
Frizzled 2, 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 2, 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 / Mainly Beta
Similarity search - Domain/homology
PALMITOLEIC ACID / Frizzled-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Frizzled-2
B: Antibody pF7_A5 Fab, Light chain
C: Antibody pF7_A5 Fab, Heavy chain
D: Frizzled-2
E: Antibody pF7_A5 Fab, Light chain
F: Antibody pF7_A5 Fab, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9479
Polymers123,2506
Non-polymers6973
Water5,675315
1
A: Frizzled-2
B: Antibody pF7_A5 Fab, Light chain
C: Antibody pF7_A5 Fab, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8464
Polymers61,6253
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-38 kcal/mol
Surface area25250 Å2
MethodPISA
2
D: Frizzled-2
E: Antibody pF7_A5 Fab, Light chain
F: Antibody pF7_A5 Fab, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1015
Polymers61,6253
Non-polymers4762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-37 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.376, 66.661, 90.912
Angle α, β, γ (deg.)95.138, 109.150, 115.328
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Antibody , 2 types, 4 molecules BECF

#2: Antibody Antibody pF7_A5 Fab, Light chain


Mass: 22477.893 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 pF7_A5 Fab, Heavy chain


Mass: 23997.920 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)

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Protein / Sugars , 2 types, 4 molecules AD

#1: Protein Frizzled-2 / Fz-2 / hFz2 / FzE2


Mass: 15149.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q14332
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 316 molecules

#5: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 8% TacsimateTM, pH 4.0 and 20% PEG 3350

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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: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.24→27.76 Å / Num. obs: 59980 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.22 Å2 / CC1/2: 0.975 / CC star: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 0.983 / Net I/σ(I): 14.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.493 / Num. unique obs: 2991 / CC1/2: 0.819 / CC star: 0.949 / Rpim(I) all: 0.331 / Rrim(I) all: 0.597 / Χ2: 1.215 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C0B

6c0b


Resolution: 2.24→27.76 Å / SU ML: 0.2246 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.5974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 2810 4.79 %
Rwork0.2155 55849 -
obs0.2168 58659 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.68 Å2
Refinement stepCycle: LAST / Resolution: 2.24→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 46 315 8687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738591
X-RAY DIFFRACTIONf_angle_d0.968911701
X-RAY DIFFRACTIONf_chiral_restr0.06651304
X-RAY DIFFRACTIONf_plane_restr0.00671516
X-RAY DIFFRACTIONf_dihedral_angle_d16.39843088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.3338860.30581792X-RAY DIFFRACTION61.01
2.28-2.320.33851250.27162433X-RAY DIFFRACTION83.21
2.32-2.370.32571310.27272707X-RAY DIFFRACTION91.76
2.37-2.410.26851180.27072780X-RAY DIFFRACTION96.06
2.41-2.470.30871590.26742905X-RAY DIFFRACTION97.02
2.47-2.520.26381350.27292841X-RAY DIFFRACTION97.54
2.52-2.590.29821640.27272836X-RAY DIFFRACTION97.98
2.59-2.660.25541550.26552878X-RAY DIFFRACTION98
2.66-2.740.2971280.25772884X-RAY DIFFRACTION97.79
2.74-2.820.33081370.25652839X-RAY DIFFRACTION98.22
2.82-2.920.27661510.25422899X-RAY DIFFRACTION98.51
2.92-3.040.30231380.2482881X-RAY DIFFRACTION98.56
3.04-3.180.27221150.2372942X-RAY DIFFRACTION98.58
3.18-3.350.2461460.22562874X-RAY DIFFRACTION98.85
3.35-3.560.23281050.21512926X-RAY DIFFRACTION98.76
3.56-3.830.20121350.19812888X-RAY DIFFRACTION99.15
3.83-4.210.19812040.18032854X-RAY DIFFRACTION99.12
4.22-4.820.21590.15822910X-RAY DIFFRACTION99.35
4.82-6.060.20171540.17492909X-RAY DIFFRACTION99.64
6.07-27.760.20761650.17112871X-RAY DIFFRACTION98.99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5125274058-0.9792919996650.6489952045461.42952239743-0.3292589804772.00093274074-0.077013707392-0.119135903770.05743208327160.1885920289090.05405176356960.124826416844-0.162070309294-0.07561548808150.001353701019140.17057192973-0.006947885742090.04534826713830.1579693785480.02760162613880.208931896426-10.6404721664-39.135395622893.1244571472
20.8970457179340.3553528274981.101013396020.08641251682040.7533223876022.09853353906-0.2913480528510.189932755640.265551309973-0.212538939813-0.0458296413850.0719342610896-0.6861048226950.1915827805710.3024021701760.416332604144-0.0253785044848-0.08095625953230.2033451450120.02548149302220.32318021832311.9362062287-30.6530815873138.709450333
30.493164769910.09918716601380.2703567308270.3578950394970.2240491002022.973902184830.03777234858160.02558985062710.076851718042-0.0384889916156-0.04848164410660.022435671331-0.109556855954-0.3450972873140.02240797409080.1853648326070.04277741248090.02018084872630.188338828866-0.01584097524550.225685191333-1.57465731385-42.4644553921139.999030286
42.28739194811-0.4867142610330.6561769246411.18337621588-0.5829812396442.162753592010.003084345395380.242654927529-0.0736229349621-0.0209167694014-0.0602477173342-0.159741548982-0.005848786765730.2443042326870.05440106647380.199205308551-0.00399448995896-0.003321853083640.222011232404-0.03810857814570.250490202225-9.74366798782-39.641772240357.7697337615
5-0.156670302792-0.0338406417956-0.2692124994810.956781026526-1.321474816092.18801444122-0.0641674133285-0.1559544848660.04054459570040.31400715732-0.267510623953-0.236770844615-0.4856874211890.5200489121910.2700752724660.276499242931-0.104733319237-0.04338997931810.4094369256890.07034840322130.340663743699-11.9201375843-15.623227919812.4919503031
60.4985882946520.0293330450780.0463987633740.455687081537-0.4341647484723.046657647220.00375506027617-0.1090459174430.0224478591387-0.02707932628320.0159088413773-0.0462668533450.2855215335230.2628767032510.009177826749030.1715165957130.03081292427080.02844554012790.202186659758-0.01203928778780.219881435885-16.7353248343-32.959029069511.2035978204
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 37 through 301)AA - C37 - 3011
22(chain 'B' and resid 1 through 209)BD1 - 2091 - 209
33(chain 'C' and resid 1 through 227)CE1 - 2271 - 227
44(chain 'D' and resid 37 through 201)DF - G37 - 2011
55(chain 'E' and resid 1 through 209)EH1 - 2091 - 209
66(chain 'F' and resid 1 through 227)FI1 - 2271 - 227

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