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- PDB-5uwg: The crystal structure of Fz4-CRD in complex with palmitoleic acid -

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Basic information

Entry
Database: PDB / ID: 5uwg
TitleThe crystal structure of Fz4-CRD in complex with palmitoleic acid
ComponentsFrizzled-4
KeywordsSIGNALING PROTEIN / Wnt / Frizzled / signalosome / cysteine-rich domain / Wnt5a / Wnt8 / Frizzled-4
Function / homology
Function and homology information


cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / retinal blood vessel morphogenesis / locomotion involved in locomotory behavior / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / Signaling by RNF43 mutants ...cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / retinal blood vessel morphogenesis / locomotion involved in locomotory behavior / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / Wnt receptor activity / endothelial cell differentiation / Wnt-protein binding / establishment of blood-brain barrier / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / positive regulation of dendrite morphogenesis / cytokine receptor activity / cytokine binding / canonical Wnt signaling pathway / vasculogenesis / cellular response to retinoic acid / Regulation of FZD by ubiquitination / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / cellular response to leukemia inhibitory factor / PDZ domain binding / G protein-coupled receptor activity / sensory perception of sound / clathrin-coated endocytic vesicle membrane / neuron differentiation / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Ca2+ pathway / signaling receptor activity / amyloid-beta binding / angiogenesis / cell population proliferation / response to hypoxia / positive regulation of cell migration / protein heterodimerization activity / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / plasma membrane
Similarity search - Function
Frizzled-4 / Frizzled 4, cysteine-rich 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-4 / Frizzled 4, cysteine-rich 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PALMITOLEIC ACID / Frizzled-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsKe, J. / DeBruine, Z.J. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR053293 United States
Van Andel Research Institute Foundation United States
CitationJournal: Genes Dev. / Year: 2017
Title: Wnt5a promotes Frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerization.
Authors: DeBruine, Z.J. / Ke, J. / Harikumar, K.G. / Gu, X. / Borowsky, P. / Williams, B.O. / Xu, W. / Miller, L.J. / Xu, H.E. / Melcher, K.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 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 1.4Oct 4, 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: Frizzled-4
B: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2136
Polymers28,2952
Non-polymers9184
Water1086
1
A: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8444
Polymers14,1471
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3692
Polymers14,1471
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.452, 109.373, 76.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Frizzled-4 / hFz4 / FzE4


Mass: 14147.333 Da / Num. of mol.: 2 / Fragment: Cysteine Rich Domain (UNP residues 40-164)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9ULV1
#2: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#3: 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.: 3
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.6 Å3/Da / Density % sol: 66 %
Description: Rod-shaped crystal with the longest dimension of 0.15 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M citric acid pH 3.5, 28% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 14355 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.3
Reflection shellResolution: 2.56→2.67 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / Num. unique obs: 1739 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CM4

5cm4


Resolution: 2.56→30.83 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 744 5.19 %
Rwork0.2444 --
obs0.2456 14334 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→30.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 60 6 1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081859
X-RAY DIFFRACTIONf_angle_d1.1162505
X-RAY DIFFRACTIONf_dihedral_angle_d15.832690
X-RAY DIFFRACTIONf_chiral_restr0.044283
X-RAY DIFFRACTIONf_plane_restr0.008320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5601-2.75760.31421550.31032670X-RAY DIFFRACTION100
2.7576-3.03490.32221770.30422656X-RAY DIFFRACTION100
3.0349-3.47360.3368990.27882746X-RAY DIFFRACTION100
3.4736-4.37430.24781640.24052707X-RAY DIFFRACTION100
4.3743-30.83190.25341490.22352811X-RAY DIFFRACTION99

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