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- PDB-6o3b: Crystal structure of Frizzled 7 CRD in complex with F6 Fab -

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Basic information

Entry
Database: PDB / ID: 6o3b
TitleCrystal structure of Frizzled 7 CRD in complex with F6 Fab
Components
  • (Antibody Fab F6, ...) x 2
  • Frizzled-7
KeywordsSIGNALING PROTEIN / Receptor / Wnt / Frizzled / CRD / Antibody
Function / homology
Function and homology information


negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / somatic stem cell division / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / somatic stem cell division / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / regulation of canonical Wnt signaling pathway / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / canonical Wnt signaling pathway / positive regulation of phosphorylation / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / G protein-coupled receptor activity / PDZ domain binding / positive regulation of JNK cascade / neuron differentiation / recycling endosome membrane / T cell differentiation in thymus / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / membrane / plasma membrane
Similarity search - Function
Frizzled-7, cysteine-rich Wnt-binding 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-7, cysteine-rich Wnt-binding 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRaman, S. / Beilschmidt, M. / Fransson, J. / Julien, J.P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies.
Authors: Raman, S. / Beilschmidt, M. / To, M. / Lin, K. / Lui, F. / Jmeian, Y. / Ng, M. / Fernandez, M. / Fu, Y. / Mascall, K. / Duque, A. / Wang, X. / Pan, G. / Angers, S. / Moffat, J. / Sidhu, S.S. ...Authors: Raman, S. / Beilschmidt, M. / To, M. / Lin, K. / Lui, F. / Jmeian, Y. / Ng, M. / Fernandez, M. / Fu, Y. / Mascall, K. / Duque, A. / Wang, X. / Pan, G. / Angers, S. / Moffat, J. / Sidhu, S.S. / Magram, J. / Sinclair, A.M. / Fransson, J. / Julien, J.P.
History
DepositionFeb 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Fab F6, Light chain
B: Antibody Fab F6, Heavy chain
C: Frizzled-7
E: Antibody Fab F6, Light chain
G: Antibody Fab F6, Heavy chain
H: Frizzled-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,85913
Polymers123,9566
Non-polymers9037
Water2,936163
1
A: Antibody Fab F6, Light chain
B: Antibody Fab F6, Heavy chain
C: Frizzled-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4767
Polymers61,9783
Non-polymers4974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-40 kcal/mol
Surface area24920 Å2
MethodPISA
2
E: Antibody Fab F6, Light chain
G: Antibody Fab F6, Heavy chain
H: Frizzled-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3846
Polymers61,9783
Non-polymers4053
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-34 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.642, 85.848, 104.103
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules AEBG

#1: Antibody Antibody Fab F6, Light chain


Mass: 23360.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody Fab F6, Heavy chain


Mass: 23402.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 4 molecules CH

#3: Protein Frizzled-7 / hFz7 / FzE3


Mass: 15215.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Production host: Homo sapiens (human) / References: UniProt: O75084
#5: 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: isolated from a genetically manipulated source
Formula: C8H15NO6
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, 168 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.2 M Na2HPO4, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03327 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03327 Å / Relative weight: 1
ReflectionResolution: 2.5→29.74 Å / Num. obs: 41997 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.975 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.128 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.011 / CC1/2: 0.659 / Rpim(I) all: 0.627

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XPREPdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O3A

6o3a


Resolution: 2.5→29.737 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1998 4.76 %
Rwork0.248 --
obs0.2497 41964 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 58 163 8641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028701
X-RAY DIFFRACTIONf_angle_d0.5411855
X-RAY DIFFRACTIONf_dihedral_angle_d15.9535200
X-RAY DIFFRACTIONf_chiral_restr0.0431321
X-RAY DIFFRACTIONf_plane_restr0.0041519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.39091430.3592872X-RAY DIFFRACTION100
2.5625-2.63170.39461440.36042858X-RAY DIFFRACTION100
2.6317-2.70910.3791430.33592879X-RAY DIFFRACTION100
2.7091-2.79650.40611430.33472840X-RAY DIFFRACTION99
2.7965-2.89640.36471430.32582868X-RAY DIFFRACTION100
2.8964-3.01230.4151430.32712866X-RAY DIFFRACTION100
3.0123-3.14920.3791440.29842889X-RAY DIFFRACTION100
3.1492-3.3150.29121430.27562864X-RAY DIFFRACTION99
3.315-3.52240.28031410.25572827X-RAY DIFFRACTION98
3.5224-3.79390.31191420.23722831X-RAY DIFFRACTION99
3.7939-4.17470.22641420.21932852X-RAY DIFFRACTION97
4.1747-4.77670.17311400.17552791X-RAY DIFFRACTION96
4.7767-6.010.23881420.19162832X-RAY DIFFRACTION98
6.01-29.73890.22591450.18852897X-RAY DIFFRACTION97

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