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- PDB-5t44: Crystal structure of Frizzled 7 CRD -

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Basic information

Entry
Database: PDB / ID: 5t44
TitleCrystal structure of Frizzled 7 CRD
ComponentsFrizzled-7
KeywordsIMMUNE SYSTEM / Cysteine rich domain
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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9944 Å
AuthorsMukund, S. / Nile, A.H. / Stanger, K. / Hannous, R.H. / Wang, W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding.
Authors: Nile, A.H. / Mukund, S. / Stanger, K. / Wang, W. / Hannoush, R.N.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Frizzled-7
B: Frizzled-7


Theoretical massNumber of molelcules
Total (without water)32,7972
Polymers32,7972
Non-polymers00
Water1,76598
1
A: Frizzled-7


Theoretical massNumber of molelcules
Total (without water)16,3991
Polymers16,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-16 kcal/mol
Surface area11560 Å2
MethodPISA
3
B: Frizzled-7


Theoretical massNumber of molelcules
Total (without water)16,3991
Polymers16,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.056, 62.846, 103.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Frizzled-7 / hFz7 / FzE3


Mass: 16398.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75084
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 0.1M MES at pH6.9, 12% 1-propanol, 10% PEG 500MME

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9944→36.5 Å / Num. obs: 35844 / % possible obs: 99.7 % / Redundancy: 6.4 % / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.9944→36.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 27.26
RfactorNum. reflection% reflection
Rfree0.2522 1686 5.1 %
Rwork0.1991 --
obs0.2016 33064 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9944→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 0 98 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061886
X-RAY DIFFRACTIONf_angle_d0.9442551
X-RAY DIFFRACTIONf_dihedral_angle_d15.515697
X-RAY DIFFRACTIONf_chiral_restr0.035276
X-RAY DIFFRACTIONf_plane_restr0.005341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9944-2.0530.39211340.32122515X-RAY DIFFRACTION94
2.053-2.11930.36381730.27112581X-RAY DIFFRACTION100
2.1193-2.1950.30731470.24332570X-RAY DIFFRACTION97
2.195-2.28290.39051420.33522550X-RAY DIFFRACTION98
2.2829-2.38680.26321420.2022651X-RAY DIFFRACTION100
2.3868-2.51260.22471390.19442646X-RAY DIFFRACTION100
2.5126-2.670.27151310.19652639X-RAY DIFFRACTION100
2.67-2.87610.2261280.19962658X-RAY DIFFRACTION99
2.8761-3.16530.25431640.19242603X-RAY DIFFRACTION100
3.1653-3.6230.23781430.18382637X-RAY DIFFRACTION100
3.623-4.56320.1981220.16222664X-RAY DIFFRACTION99
4.5632-36.53490.22021210.17582664X-RAY DIFFRACTION100
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)
11.3743-0.72630.79760.8147-1.18582.06250.0135-0.08850.0147-0.0696-0.0077-0.00910.1451-0.123800.2995-0.0126-0.03970.212-0.00390.1818-17.0674-5.21336.8019
21.0255-0.1910.58220.7708-0.32821.9011-0.0459-0.12120.00440.10860.12820.03280.0926-0.03620.00010.22590.0220.01190.22820.00060.2318-5.3502-11.438530.8891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 17:133
2X-RAY DIFFRACTION2chain B and resid 17:133

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