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- PDB-6o39: Crystal structure of Frizzled 5 CRD in complex with F2.I Fab -

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Basic information

Entry
Database: PDB / ID: 6o39
TitleCrystal structure of Frizzled 5 CRD in complex with F2.I Fab
Components
  • (Antibody F2.I Fab, ...) x 2
  • Frizzled-5
KeywordsSIGNALING PROTEIN / Receptor / Wnt / Frizzled / CRD / Antibody
Function / homology
Function and homology information


regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / cellular response to molecule of bacterial origin / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / chorionic trophoblast cell differentiation / embryonic camera-type eye morphogenesis / glandular epithelial cell maturation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 ...regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / cellular response to molecule of bacterial origin / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / chorionic trophoblast cell differentiation / embryonic camera-type eye morphogenesis / glandular epithelial cell maturation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / apoptotic process involved in morphogenesis / anterior/posterior axis specification, embryo / embryonic axis specification / Wnt receptor activity / regulation of mitophagy / non-canonical Wnt signaling pathway / intestinal epithelial cell maturation / Wnt-protein binding / branching involved in labyrinthine layer morphogenesis / Class B/2 (Secretin family receptors) / regulation of bicellular tight junction assembly / Disassembly of the destruction complex and recruitment of AXIN to the membrane / labyrinthine layer blood vessel development / positive regulation of protein targeting to mitochondrion / canonical Wnt signaling pathway / bicellular tight junction / synapse assembly / Regulation of FZD by ubiquitination / positive regulation of interleukin-1 beta production / Asymmetric localization of PCP proteins / G protein-coupled receptor activity / clathrin-coated endocytic vesicle membrane / neuron differentiation / positive regulation of T cell cytokine production / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / Ca2+ pathway / T cell differentiation in thymus / amyloid-beta binding / perikaryon / early endosome membrane / angiogenesis / axon / negative regulation of cell population proliferation / Golgi membrane / dendrite / synapse / lipid binding / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Frizzled-5, CRD 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-5, CRD 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
ACETATE ION / Frizzled-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody F2.I Fab, Light chain
B: Antibody F2.I Fab, Heavy chain
C: Frizzled-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,75718
Polymers60,6703
Non-polymers1,08715
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-9 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.405, 101.405, 196.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-432-

HOH

21B-485-

HOH

31B-529-

HOH

41B-540-

HOH

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody F2.I Fab, Light chain


Mass: 23218.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody F2.I Fab, Heavy chain


Mass: 23323.039 Da / Num. of mol.: 1
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, 2 molecules C

#3: Protein Frizzled-5 / / hFz5 / FzE5


Mass: 14128.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD5, C2orf31 / Production host: Homo sapiens (human) / References: UniProt: Q13467
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 3 types, 400 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→36.4798 Å / Num. obs: 56003 / % possible obs: 99.97 % / Redundancy: 20 % / Net I/σ(I): 25.13
Reflection shellResolution: 1.8→1.864 Å

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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: 4F0A

4f0a


Resolution: 1.8→36.472 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2000 3.57 %
Rwork0.1963 --
obs0.1976 55999 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 70 386 4654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064466
X-RAY DIFFRACTIONf_angle_d0.8816081
X-RAY DIFFRACTIONf_dihedral_angle_d17.8412709
X-RAY DIFFRACTIONf_chiral_restr0.057677
X-RAY DIFFRACTIONf_plane_restr0.006779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.38511410.32393817X-RAY DIFFRACTION100
1.845-1.89490.35921400.29143756X-RAY DIFFRACTION100
1.8949-1.95070.34051400.26933803X-RAY DIFFRACTION100
1.9507-2.01360.29591400.24643762X-RAY DIFFRACTION100
2.0136-2.08560.27531410.22773806X-RAY DIFFRACTION100
2.0856-2.16910.23121400.22553794X-RAY DIFFRACTION100
2.1691-2.26780.27081420.21913820X-RAY DIFFRACTION100
2.2678-2.38730.26221410.22063807X-RAY DIFFRACTION100
2.3873-2.53690.25351430.22043857X-RAY DIFFRACTION100
2.5369-2.73270.24991420.2143848X-RAY DIFFRACTION100
2.7327-3.00760.24281430.21613865X-RAY DIFFRACTION100
3.0076-3.44250.23751460.20013913X-RAY DIFFRACTION100
3.4425-4.3360.20791450.16643952X-RAY DIFFRACTION100
4.336-36.47980.18441560.15514199X-RAY DIFFRACTION100

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