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- PDB-5bpb: Crystal structure of the cysteine-rich domain of human Frizzled 4... -

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Basic information

Entry
Database: PDB / ID: 5bpb
TitleCrystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form I
ComponentsFrizzled-4
KeywordsSIGNALING PROTEIN / Wnt signalling pathway / Glycoprotein / G protein coupled receptor / receptor for Norrin recognition
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 / retina vasculature morphogenesis in camera-type eye / locomotion involved in locomotory behavior / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 ...cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / retinal blood vessel morphogenesis / retina vasculature morphogenesis in camera-type eye / locomotion involved in locomotory behavior / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 / Wnt receptor activity / regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / Wnt-protein binding / endothelial cell differentiation / establishment of blood-brain barrier / positive regulation of dendrite morphogenesis / Class B/2 (Secretin family receptors) / cytokine receptor activity / cytokine binding / negative regulation of cell-substrate adhesion / canonical Wnt signaling pathway / vasculogenesis / cellular response to retinoic acid / Regulation of FZD by ubiquitination / substrate adhesion-dependent cell spreading / cellular response to leukemia inhibitory factor / Asymmetric localization of PCP proteins / positive regulation of DNA-binding transcription factor activity / PDZ domain binding / sensory perception of sound / clathrin-coated endocytic vesicle membrane / G protein-coupled receptor activity / neuron differentiation / Wnt signaling pathway / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / amyloid-beta binding / Ca2+ pathway / angiogenesis / cell population proliferation / response to hypoxia / positive regulation of cell migration / protein heterodimerization activity / dendrite / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of DNA-templated transcription / glutamatergic synapse / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChang, T.-H. / Hsieh, F.-L. / Harlos, K. / Jones, E.Y.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0900084 United Kingdom
Cancer Research UKC375/A10976 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Elife / Year: 2015
Title: Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan.
Authors: Chang, T.H. / Hsieh, F.L. / Zebisch, M. / Harlos, K. / Elegheert, J. / Jones, E.Y.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 2.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 2.2Jan 10, 2024Group: 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
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Frizzled-4
C: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7068
Polymers66,8214
Non-polymers8854
Water2,666148
1
A: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9262
Polymers16,7051
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1483
Polymers16,7051
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9262
Polymers16,7051
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Frizzled-4


Theoretical massNumber of molelcules
Total (without water)16,7051
Polymers16,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.608, 102.140, 116.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Frizzled-4 / hFz4 / FzE4


Mass: 16705.232 Da / Num. of mol.: 4 / Fragment: UNP residues 42-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD4 / Plasmid: pHLsec-mVenus-12H / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9ULV1
#2: 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.: 4
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.6 M tri-sodium citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.2→41.77 Å / Num. obs: 44268 / % possible obs: 99.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJY

1ijy


Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.055 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 2227 5 %RANDOM
Rwork0.1767 ---
obs0.179 42000 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.02 Å2 / Biso mean: 46.189 Å2 / Biso min: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--1.19 Å20 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 70 148 4084
Biso mean--33.97 43.27 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194067
X-RAY DIFFRACTIONr_bond_other_d0.0010.023808
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9955527
X-RAY DIFFRACTIONr_angle_other_deg0.7883.0098772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71824.913173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59715683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6731517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02873
X-RAY DIFFRACTIONr_mcbond_it2.1252.1761975
X-RAY DIFFRACTIONr_mcbond_other2.0922.1761974
X-RAY DIFFRACTIONr_mcangle_it2.9033.2592460
X-RAY DIFFRACTIONr_rigid_bond_restr1.52337875
X-RAY DIFFRACTIONr_sphericity_free41.95547
X-RAY DIFFRACTIONr_sphericity_bonded10.71257852
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 161 -
Rwork0.228 3054 -
all-3215 -
obs--99.6 %
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)
15.4582-1.5197-1.04823.21051.78194.5574-0.0898-0.79210.38990.36950.0339-0.0425-0.07820.08130.05590.0785-0.0078-0.01190.1714-0.05860.03535.07337.36112.219
23.88110.9742-0.83642.9501-1.40123.491-0.07210.60060.3313-0.28630.02880.0995-0.2151-0.03730.04330.08080.0007-0.02570.14370.05190.0345-4.70338.752-12.741
32.8959-0.32111.54853.68161.56466.82280.07070.2023-0.2043-0.2036-0.12460.07570.3483-0.08960.05390.0825-0.0330.03550.108-0.06260.07494.64111.601-17.121
45.0134-1.5544.32434.4972-4.778412.58770.1945-0.3633-0.48510.2433-0.2033-0.10890.96010.23390.00870.23930.05190.03170.17510.10670.1476-6.40412.45417.941
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 162
2X-RAY DIFFRACTION2B44 - 186
3X-RAY DIFFRACTION3D43 - 172
4X-RAY DIFFRACTION4C44 - 161

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