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- PDB-6o3a: Crystal structure of Frizzled 7 CRD in complex with F7.B Fab -

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Basic information

Entry
Database: PDB / ID: 6o3a
TitleCrystal structure of Frizzled 7 CRD in complex with F7.B Fab
Components
  • (Antibody F7.B Fab, ...) 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 / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / non-canonical Wnt signaling pathway / mesenchymal to epithelial transition / 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 / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / non-canonical Wnt signaling pathway / mesenchymal to epithelial transition / 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) / regulation of canonical Wnt signaling pathway / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / positive regulation of phosphorylation / negative regulation of cell-substrate adhesion / canonical Wnt signaling pathway / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / positive regulation of JNK cascade / PDZ domain binding / G protein-coupled receptor activity / recycling endosome membrane / neuron differentiation / 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/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-7, cysteine-rich Wnt-binding 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
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
Revision 1.4Nov 20, 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: Antibody F7.B Fab, Light chain
B: Antibody F7.B Fab, Heavy chain
E: Frizzled-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,73013
Polymers61,6713
Non-polymers1,05910
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-10 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.544, 103.446, 144.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody F7.B Fab, Light chain


Mass: 23209.730 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 F7.B Fab, Heavy chain


Mass: 23404.049 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, 3 molecules E

#3: Protein Frizzled-7 / hFz7 / FzE3


Mass: 15057.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Production host: Homo sapiens (human) / References: UniProt: O75084
#7: 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 , 4 types, 315 molecules

#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10
Details: 0.1 M CAPS, pH 10.5, 20% (w/v) PEG 3350, 0.2 M NaCl

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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: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→38.551 Å / Num. obs: 37237 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 1.12 / CC1/2: 0.701 / Rpim(I) all: 0.438

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XPREPdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bpq

5bpq


Resolution: 2.1→38.551 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 1862 5 %
Rwork0.1919 --
obs0.1943 37227 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→38.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 67 307 4575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074385
X-RAY DIFFRACTIONf_angle_d0.945965
X-RAY DIFFRACTIONf_dihedral_angle_d17.4122617
X-RAY DIFFRACTIONf_chiral_restr0.054665
X-RAY DIFFRACTIONf_plane_restr0.006759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.33911400.26542668X-RAY DIFFRACTION100
2.1568-2.22030.28771420.2482685X-RAY DIFFRACTION100
2.2203-2.29190.28981410.2582666X-RAY DIFFRACTION100
2.2919-2.37380.28221400.2382660X-RAY DIFFRACTION100
2.3738-2.46880.30871430.23152713X-RAY DIFFRACTION100
2.4688-2.58120.28431410.22012703X-RAY DIFFRACTION100
2.5812-2.71720.25911420.20842677X-RAY DIFFRACTION100
2.7172-2.88740.27081410.21462694X-RAY DIFFRACTION100
2.8874-3.11030.30591430.21632712X-RAY DIFFRACTION100
3.1103-3.42310.21741440.20052733X-RAY DIFFRACTION100
3.4231-3.9180.24511440.18062739X-RAY DIFFRACTION100
3.918-4.93470.18291470.14362788X-RAY DIFFRACTION100
4.9347-38.55780.19361540.16152927X-RAY DIFFRACTION100

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