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- PDB-1ijy: CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8... -

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Basic information

Entry
Database: PDB / ID: 1ijy
TitleCRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 (MFZ8)
ComponentsFRIZZLED HOMOLOG 8
KeywordsSIGNALING PROTEIN / WNT RECEPTOR / FRIZZLED PROTEIN STRUCTURE / CYSTEINE-RICH
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / Wnt-protein binding / canonical Wnt signaling pathway / neuronal dense core vesicle / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway ...Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / Wnt-protein binding / canonical Wnt signaling pathway / neuronal dense core vesicle / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway / T cell differentiation in thymus / angiogenesis / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / extracellular region / plasma membrane
Similarity search - Function
Frizzled 8, 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 ...Frizzled 8, 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDann III, C.E. / Hsieh, J.C. / Rattner, A. / Sharma, D. / Nathans, J. / Leahy, D.J.
CitationJournal: Nature / Year: 2001
Title: Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains.
Authors: Dann III, C.E. / Hsieh, J.C. / Rattner, A. / Sharma, D. / Nathans, J. / Leahy, D.J.
History
DepositionMay 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 28, 2014Group: Structure summary
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRIZZLED HOMOLOG 8
B: FRIZZLED HOMOLOG 8


Theoretical massNumber of molelcules
Total (without water)29,8862
Polymers29,8862
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.69, 36.37, 57.94
Angle α, β, γ (deg.)90, 98.82, 90
Int Tables number3
Space group name H-MP121

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Components

#1: Protein FRIZZLED HOMOLOG 8


Mass: 14943.059 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH DOMAIN / Mutation: N22E, N125E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: FZD8 / Plasmid: PSGHV0 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q61091
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Ammonium Sulfate, Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
21.9 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 50707 / Num. obs: 48062 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.5
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4993 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IJX

1ijx


Resolution: 1.35→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4898 -RANDOM
Rwork0.225 ---
all-50707 --
obs-48062 94.8 %-
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 0 279 2257
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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