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- PDB-5bqc: Crystal structure of Norrin in complex with the cysteine-rich dom... -

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Basic information

Entry
Database: PDB / ID: 5bqc
TitleCrystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate
Components
  • Frizzled-4
  • Norrin
KeywordsSIGNALING PROTEIN / Wnt signalling pathway / Norrie disease protein / Glycoprotein / G protein coupled receptor
Function / homology
Function and homology information


cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation ...cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / retina vasculature morphogenesis in camera-type eye / locomotion involved in locomotory behavior / Signaling by RNF43 mutants / ubiquitin-dependent endocytosis / WNT5A-dependent internalization of FZD4 / glycine metabolic process / regulation of vascular endothelial growth factor receptor signaling pathway / retina layer formation / positive regulation of neuron projection arborization / Wnt receptor activity / retinal pigment epithelium development / non-canonical Wnt signaling pathway / endothelial cell differentiation / microglial cell proliferation / Wnt-protein binding / dendritic spine development / establishment of blood-retinal barrier / vacuole organization / protein targeting to lysosome / positive regulation of dendrite morphogenesis / microglia differentiation / establishment of blood-brain barrier / optic nerve development / frizzled binding / Class B/2 (Secretin family receptors) / retinal ganglion cell axon guidance / cytokine receptor activity / lens development in camera-type eye / smoothened signaling pathway / cytokine binding / exploration behavior / decidualization / action potential / blood vessel remodeling / negative regulation of cell-substrate adhesion / canonical Wnt signaling pathway / response to axon injury / Regulation of FZD by ubiquitination / vasculogenesis / cellular response to retinoic acid / tricarboxylic acid cycle / visual perception / glutathione metabolic process / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / cytokine activity / PDZ domain binding / sensory perception of sound / clathrin-coated endocytic vesicle membrane / G protein-coupled receptor activity / Wnt signaling pathway / neuron differentiation / Cargo recognition for clathrin-mediated endocytosis / cell-cell junction / Clathrin-mediated endocytosis / nervous system development / mitotic cell cycle / signaling receptor activity / : / amyloid-beta binding / Ca2+ pathway / neuron apoptotic process / angiogenesis / cellular response to hypoxia / transcription by RNA polymerase II / response to hypoxia / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cilium / positive regulation of cell migration / inflammatory response / protein heterodimerization activity / ubiquitin protein ligase binding / dendrite / positive regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / plasma membrane
Similarity search - Function
Frizzled-4 / Frizzled 4, cysteine-rich domain / Norrie disease protein / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Glycoprotein hormone subunit beta / Cystine-knot domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region ...Frizzled-4 / Frizzled 4, cysteine-rich domain / Norrie disease protein / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Glycoprotein hormone subunit beta / Cystine-knot domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / C-terminal cystine knot signature. / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
sucrose octasulfate / Norrin / Frizzled-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsChang, T.-H. / Hsieh, F.-L. / Zebisch, M. / 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_symm_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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Frizzled-4
A: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7455
Polymers30,3202
Non-polymers1,4253
Water00
1
B: Frizzled-4
A: Norrin
hetero molecules

B: Frizzled-4
A: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49010
Polymers60,6404
Non-polymers2,8506
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area8290 Å2
ΔGint-33 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.136, 119.136, 119.151
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Frizzled-4 / hFz4 / FzE4


Mass: 16705.232 Da / Num. of mol.: 1 / Fragment: 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: Protein Norrin / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 13614.706 Da / Num. of mol.: 1 / Fragment: residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: homo sapiens (human) / References: UniProt: Q00604
#3: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#4: 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.: 2
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

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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: 4.03 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.0, 0.15 M NaCl, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→47.34 Å / Num. obs: 10503 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.031 / Net I/σ(I): 14.6 / Num. measured all: 205532 / Scaling rejects: 18
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
3-3.1820.62.461.63402616480.1490.548100
9-47.3416.80.04950.278344650.9990.01399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.57 Å42.12 Å
Translation5.57 Å42.12 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
PHASER2.5.6phasing
REFMAC5.8.0069refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPB,5BPU

5bpb

5bpu


Resolution: 3→47.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 571 5.5 %RANDOM
Rwork0.2147 ---
obs0.2175 9904 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.16 Å2 / Biso mean: 113.96 Å2 / Biso min: 65.73 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å2-1.5 Å20 Å2
2---3 Å20 Å2
3---9.74 Å2
Refinement stepCycle: final / Resolution: 3→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 83 0 1842
Biso mean--112.7 --
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191894
X-RAY DIFFRACTIONr_bond_other_d0.0030.021720
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.022577
X-RAY DIFFRACTIONr_angle_other_deg0.9353.0063984
X-RAY DIFFRACTIONr_chiral_restr0.050.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02416
X-RAY DIFFRACTIONr_mcbond_it5.2837.828894
X-RAY DIFFRACTIONr_mcbond_other5.287.826893
X-RAY DIFFRACTIONr_mcangle_it7.39711.7221114
X-RAY DIFFRACTIONr_rigid_bond_restr1.0833612
X-RAY DIFFRACTIONr_sphericity_free39.74852
X-RAY DIFFRACTIONr_sphericity_bonded22.40653562
LS refinement shellResolution: 3→3.078 Å
RfactorNum. reflection% reflection
Rfree0.45 48 -
Rwork0.35 685 -
obs--100 %
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)
14.7769-0.86360.96527.8459-3.77665.92650.12830.43080.3069-0.4207-0.06820.258-0.072-0.0085-0.06020.12840.0824-0.02930.3001-0.03840.0495-6.707-35.229-8.174
23.2197-1.4125-3.68880.91832.07235.8745-0.20740.3353-0.15550.23170.10130.14840.4087-0.29560.10610.18090.14770.01670.46220.04370.1049-18.824-48.94510.44
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 166
2X-RAY DIFFRACTION2A34 - 133

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