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- PDB-4f0a: Crystal structure of XWnt8 in complex with the cysteine-rich doma... -

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Basic information

Entry
Database: PDB / ID: 4f0a
TitleCrystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8
Components
  • Frizzled-8
  • Protein Wnt-8
KeywordsSIGNALING PROTEIN / Wnt signaling / Ligand-receptor complex / Wnt / Frizzled / Fatty acid acylation / Glycosylation
Function / homology
Function and homology information


negative regulation of cardiac cell fate specification / Spemann organizer formation / neural crest cell fate commitment / Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / embryonic axis specification / non-canonical Wnt signaling pathway / Wnt receptor activity / Wnt-protein binding ...negative regulation of cardiac cell fate specification / Spemann organizer formation / neural crest cell fate commitment / Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / embryonic axis specification / non-canonical Wnt signaling pathway / Wnt receptor activity / Wnt-protein binding / frizzled binding / anterior/posterior axis specification / neuronal dense core vesicle / canonical Wnt signaling pathway / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / T cell differentiation in thymus / angiogenesis / collagen-containing extracellular matrix / protease binding / positive regulation of protein phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane
Similarity search - Function
Wnt (Wingless and Int-1), C-terminal domain / Endo-n-acetylneuraminidase fold / Wnt-8 protein / Protein Wnt-8A/8C / Frizzled 8, cysteine-rich domain / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family ...Wnt (Wingless and Int-1), C-terminal domain / Endo-n-acetylneuraminidase fold / Wnt-8 protein / Protein Wnt-8A/8C / Frizzled 8, cysteine-rich domain / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1 / 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. / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PALMITOLEIC ACID / Protein Wnt-8 / Frizzled-8
Similarity search - Component
Biological speciesMus musculus (house mouse)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.25 Å
AuthorsJanda, C.Y. / Waghray, D. / Levin, A.M. / Thomas, C. / Garcia, K.C.
CitationJournal: Science / Year: 2012
Title: Structural basis of Wnt recognition by Frizzled.
Authors: Janda, C.Y. / Waghray, D. / Levin, A.M. / Thomas, C. / Garcia, K.C.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 25, 2013Group: Derived calculations / Non-polymer description
Revision 1.3Oct 9, 2013Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Frizzled-8
B: Protein Wnt-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6049
Polymers50,2472
Non-polymers2,3567
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.070, 110.070, 82.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Frizzled-8 / Fz-8 / mFz8


Mass: 15061.343 Da / Num. of mol.: 1 / Fragment: cysteine-rich domain, UNP residues 28-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd8 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q61091
#2: Protein Protein Wnt-8 / XWnt-8


Mass: 35185.945 Da / Num. of mol.: 1 / Fragment: UNP residues 23-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: wnt8 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P28026

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Sugars , 3 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 4.99 Å3/Da / Density % sol: 75.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 4-10 % (w/v) PEG 400 15-25 mM Zinc acetate 100 mM Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03325 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03325 Å / Relative weight: 1
ReflectionResolution: 3.25→28.64 Å / Num. obs: 29898 / % possible obs: 97.7 % / Redundancy: 2.3 % / Rsym value: 0.064 / Net I/σ(I): 12.4
Reflection shellResolution: 3.25→3.3 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.582 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.25→28.64 Å / SU ML: 0.41 / σ(F): 1.11 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1499 5.01 %
Rwork0.2035 --
obs0.2051 29898 97.77 %
all-30618 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.166 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1583 Å20 Å2-0 Å2
2--6.1583 Å20 Å2
3----12.3166 Å2
Refinement stepCycle: LAST / Resolution: 3.25→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 145 0 3334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053423
X-RAY DIFFRACTIONf_angle_d0.884614
X-RAY DIFFRACTIONf_dihedral_angle_d22.4581284
X-RAY DIFFRACTIONf_chiral_restr0.267515
X-RAY DIFFRACTIONf_plane_restr0.003586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2502-3.35490.3051340.30582629X-RAY DIFFRACTION99
3.3549-3.47460.30851440.26852560X-RAY DIFFRACTION98
3.4746-3.61350.34421280.25132665X-RAY DIFFRACTION98
3.6135-3.77760.31981700.23992520X-RAY DIFFRACTION98
3.7776-3.97630.26881490.222554X-RAY DIFFRACTION97
3.9763-4.22470.20961430.19822550X-RAY DIFFRACTION98
4.2247-4.54970.24131110.17332629X-RAY DIFFRACTION98
4.5497-5.00540.20961330.17572568X-RAY DIFFRACTION98
5.0054-5.72460.19481370.19272588X-RAY DIFFRACTION98
5.7246-7.19350.2375830.18812619X-RAY DIFFRACTION98
7.1935-28.64510.19181670.18742517X-RAY DIFFRACTION96

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