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- PDB-5urz: Crystal structure of Frizzled 5 CRD in complex with BOG -

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Basic information

Entry
Database: PDB / ID: 5urz
TitleCrystal structure of Frizzled 5 CRD in complex with BOG
ComponentsFrizzled-5
KeywordsSIGNALING PROTEIN / Frizzled 5 / CRD
Function / homology
Function and homology information


regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / cellular response to molecule of bacterial origin / embryonic camera-type eye morphogenesis / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / glandular epithelial cell maturation / chorionic trophoblast cell differentiation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / apoptotic process involved in morphogenesis ...regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / cellular response to molecule of bacterial origin / embryonic camera-type eye morphogenesis / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / glandular epithelial cell maturation / chorionic trophoblast cell differentiation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / apoptotic process involved in morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / anterior/posterior axis specification, embryo / embryonic axis specification / Wnt receptor activity / intestinal epithelial cell maturation / regulation of mitophagy / non-canonical Wnt signaling pathway / eye development / branching involved in labyrinthine layer morphogenesis / Wnt-protein binding / regulation of bicellular tight junction assembly / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of protein targeting to mitochondrion / labyrinthine layer blood vessel development / bicellular tight junction / canonical Wnt signaling pathway / synapse assembly / Regulation of FZD by ubiquitination / positive regulation of interleukin-1 beta production / Asymmetric localization of PCP proteins / G protein-coupled receptor activity / clathrin-coated endocytic vesicle membrane / positive regulation of T cell cytokine production / neuron differentiation / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / amyloid-beta binding / Ca2+ pathway / early endosome membrane / T cell differentiation in thymus / perikaryon / angiogenesis / negative regulation of cell population proliferation / Golgi membrane / axon / lipid binding / ubiquitin protein ligase binding / dendrite / synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Frizzled-5, CRD 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-5, CRD 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: 2.202 Å
AuthorsMukund, S. / Nile, A.H. / Stanger, K. / Hannoush, R.N. / 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
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Frizzled-5
B: Frizzled-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3444
Polymers33,5382
Non-polymers8062
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.051, 123.051, 46.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

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Components

#1: Protein Frizzled-5 / hFz5 / FzE5


Mass: 16769.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD5, C2orf31 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13467
#2: Polysaccharide alpha-L-fucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 513.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-L-Fucp]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dehydrate pH 5.5, 22% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20901 / % possible obs: 99.9 % / Redundancy: 10.8 % / Net I/σ(I): 25.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.202→29.556 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1070 5.12 %
Rwork0.1796 --
obs0.1818 20889 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→29.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 54 97 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112046
X-RAY DIFFRACTIONf_angle_d1.2152762
X-RAY DIFFRACTIONf_dihedral_angle_d15.788792
X-RAY DIFFRACTIONf_chiral_restr0.045298
X-RAY DIFFRACTIONf_plane_restr0.006356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2017-2.30190.24251410.22052434X-RAY DIFFRACTION100
2.3019-2.42320.24911310.19792443X-RAY DIFFRACTION100
2.4232-2.57490.23071380.18972463X-RAY DIFFRACTION100
2.5749-2.77360.25521440.19822444X-RAY DIFFRACTION100
2.7736-3.05240.24441180.20432476X-RAY DIFFRACTION100
3.0524-3.49350.27291360.18812471X-RAY DIFFRACTION100
3.4935-4.39910.17061230.15922524X-RAY DIFFRACTION100
4.3991-29.55850.21811390.17022564X-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)
10.49060.1265-0.19060.70120.96081.71670.08380.1737-0.1438-0.108-0.0885-0.00690.2579-0.15990.00030.3206-0.107-0.02680.3992-0.03190.2926-38.582345.7349-7.7263
21.49081.0340.11631.3807-0.40950.8351-0.0845-0.31970.29320.04130.12880.2895-0.0799-0.1745-00.237-0.01560.01080.4465-0.01820.4051-53.003662.9810.7878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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