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

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Basic information

Entry
Database: PDB / ID: 5bpq
TitleCrystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form II
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 / locomotion involved in locomotory behavior / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / Signaling by RNF43 mutants ...cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / retinal blood vessel morphogenesis / locomotion involved in locomotory behavior / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 / Wnt receptor activity / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / Wnt-protein binding / endothelial cell differentiation / establishment of blood-brain barrier / Class B/2 (Secretin family receptors) / positive regulation of dendrite morphogenesis / negative regulation of cell-substrate adhesion / cytokine receptor activity / cytokine binding / vasculogenesis / canonical Wnt signaling pathway / 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 / G protein-coupled receptor activity / PDZ domain binding / positive regulation of DNA-binding transcription factor activity / sensory perception of sound / clathrin-coated endocytic vesicle membrane / neuron differentiation / Wnt signaling pathway / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / signaling receptor activity / Ca2+ pathway / amyloid-beta binding / angiogenesis / cell population proliferation / response to hypoxia / positive regulation of cell migration / protein heterodimerization activity / glutamatergic synapse / dendrite / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of DNA-templated transcription / 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 / molecular replacement / Resolution: 2.4 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 28, 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 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / 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 1.5Jan 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 1.6Oct 23, 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-4
B: Frizzled-4
C: Frizzled-4
D: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7419
Polymers66,8214
Non-polymers9205
Water1,24369
1
A: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9623
Polymers16,7051
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
3
C: 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
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
Unit cell
Length a, b, c (Å)76.075, 76.075, 204.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Frizzled-4 / hFz4 / FzE4


Mass: 16705.232 Da / Num. of mol.: 4 / Fragment: cysteine-rich domain, 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 / hFz4 / FzE4 / 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 / Fragment: cysteine-rich domain, UNP residues 42-179
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Gene: FZD4 / Plasmid: pHLsec-mVenus-12H / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 0.1 M NaCl, 1.6 M ammonium sulfate

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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: 2.4→47.37 Å / Num. obs: 25975 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.026 / Net I/σ(I): 14.5 / Num. measured all: 103121
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.494.10.6062.21115727240.8140.33999.4
8.98-47.373.60.02237.717734900.9990.01395.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.4 Å47.37 Å
Translation2.4 Å47.37 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
Aimless0.1.29data scaling
PHASER2.5.6phasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPB

5bpb


Resolution: 2.4→65.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.577 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 1322 5.1 %RANDOM
Rwork0.2037 ---
obs0.2058 24639 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.44 Å2 / Biso mean: 74.887 Å2 / Biso min: 28.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----2.15 Å2
Refinement stepCycle: final / Resolution: 2.4→65.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 1 69 3835
Biso mean--87.11 68.41 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193885
X-RAY DIFFRACTIONr_bond_other_d0.0010.023599
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.9875278
X-RAY DIFFRACTIONr_angle_other_deg0.76238344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07424.969163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57815653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1541515
X-RAY DIFFRACTIONr_chiral_restr0.0590.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_mcbond_it0.9723.251896
X-RAY DIFFRACTIONr_mcbond_other0.9713.2491895
X-RAY DIFFRACTIONr_mcangle_it1.2694.8692363
X-RAY DIFFRACTIONr_rigid_bond_restr0.70837484
X-RAY DIFFRACTIONr_sphericity_free43.226544
X-RAY DIFFRACTIONr_sphericity_bonded4.65457390
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 94 -
Rwork0.287 1833 -
all-1927 -
obs--99.07 %
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)
13.6435-0.8246-0.54633.47340.96842.8359-0.0071-0.04910.045-0.10850.0077-0.2951-0.00450.2828-0.00050.0081-0.0032-0.03290.3299-0.09990.564267.373649.50079.4576
25.81311.96330.37423.43240.92982.3204-0.0637-0.07560.0210.15090.1080.30380.138-0.3001-0.04430.05260.0603-0.05180.4974-0.07580.6759105.137749.64899.3538
34.9968-0.76620.18675.81550.65182.94020.05360.18470.6059-0.0825-0.18560.5533-0.8719-0.59620.1320.37540.0902-0.01830.4407-0.06960.64384.532212.208823.2084
42.50280.5028-0.67673.3712-0.04725.98320.143-0.3244-0.47650.3294-0.17520.11180.6296-0.05630.03220.1871-0.0204-0.09580.25510.03990.627650.102430.61338.3165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 162
2X-RAY DIFFRACTION2B44 - 162
3X-RAY DIFFRACTION3C45 - 162
4X-RAY DIFFRACTION4D44 - 162

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