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

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Basic information

Entry
Database: PDB / ID: 5bqe
TitleCrystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 -Methylated form
Components
  • (Norrin) x 2
  • Frizzled-4
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 / retinal ganglion cell axon guidance / cytokine receptor activity / Class B/2 (Secretin family receptors) / 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 / vasculogenesis / response to axon injury / cellular response to retinoic acid / tricarboxylic acid cycle / visual perception / glutathione metabolic process / Regulation of FZD by ubiquitination / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / cytokine activity / Asymmetric localization of PCP proteins / PDZ domain binding / clathrin-coated endocytic vesicle membrane / sensory perception of sound / G protein-coupled receptor activity / Wnt signaling pathway / neuron differentiation / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / nervous system development / mitotic cell cycle / signaling receptor activity / Clathrin-mediated endocytosis / : / 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 / dendrite / ubiquitin protein ligase binding / 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. / C-terminal cystine knot domain profile. / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,7148
Polymers44,0973
Non-polymers6175
Water2,072115
1
A: Norrin
B: Norrin
C: Frizzled-4
hetero molecules

C: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,85012
Polymers60,8564
Non-polymers9948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,-y-1,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)98.920, 98.920, 120.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 3 types, 3 molecules ABC

#1: 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
#2: Protein Norrin / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 13722.891 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: Protein Frizzled-4 / hFz4 / FzE4


Mass: 16759.324 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

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Sugars , 1 types, 1 molecules

#5: 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.: 1
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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Non-polymers , 3 types, 119 molecules

#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine, pH 9.0, 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→49.46 Å / Num. obs: 26816 / % possible obs: 98.9 % / Redundancy: 6 % / Biso Wilson estimate: 48.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Net I/σ(I): 10.7 / Num. measured all: 161410 / Scaling rejects: 9
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
2.3-2.385.61.2121.41403725140.2880.56197.2
8.91-49.465.10.03430.627735490.9990.01698.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å49.46 Å
Translation2.3 Å49.46 Å

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
MOSFLMdata reduction
PHASER2.5.2phasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPB,5BPU

5bpb

5bpu


Resolution: 2.3→49.46 Å / FOM work R set: 0.7608 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1345 5.02 %Random selection
Rwork0.1966 25458 --
obs0.1978 26803 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.26 Å2 / Biso mean: 63.08 Å2 / Biso min: 30.05 Å2
Refinement stepCycle: final / Resolution: 2.3→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 39 115 2711
Biso mean--74.44 57.06 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042665
X-RAY DIFFRACTIONf_angle_d0.9273559
X-RAY DIFFRACTIONf_chiral_restr0.039383
X-RAY DIFFRACTIONf_plane_restr0.003455
X-RAY DIFFRACTIONf_dihedral_angle_d17.341028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.38230.35211400.32882416255697
2.3823-2.47770.35831390.30792498263798
2.4777-2.59040.26881220.27212492261498
2.5904-2.7270.29021300.25462511264198
2.727-2.89780.26261380.24542523266199
2.8978-3.12160.21821260.22272532265899
3.1216-3.43560.22891490.19982528267799
3.4356-3.93260.22521420.17242565270799
3.9326-4.95390.17261280.14062623275199
4.9539-49.47140.17811310.18642770290199
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)
11.3224-0.09480.03831.2739-0.3183-0.2811-0.1541-0.18510.0324-0.3046-0.00990.5456-0.0505-0.2043-0.0010.51330.0254-0.0480.3580.01420.3175-15.6448-34.7305-6.8736
21.7321-0.5548-0.43863.3845-3.04883.1797-0.2218-0.6999-0.38281.1860.6492-0.8012-0.42762.0732-0.2470.49150.1293-0.11820.914-0.0640.71791.071-69.0431-9.9434
31.7661-0.27330.05110.6978-0.345-0.7765-0.1855-0.08340.21580.04050.20370.0076-0.0227-0.05820.00710.47230.0187-0.05080.2399-0.01180.2398-6.3333-31.2301-3.2528
41.2399-0.2191-0.03020.2410.125-0.03620.2491-0.1821-0.5291-1.3584-0.1053-0.56610.05880.0503-0.00060.685-0.1163-0.02040.38080.03720.4207-7.5047-42.1372-14.0401
50.2805-0.02320.52720.90160.59480.9935-0.02290.8250.0919-0.052-0.43950.4830.0713-0.7316-0.05530.27490.004-0.05940.4136-0.01390.4746-18.5396-63.7011-18.1329
60.23510.12990.12370.69320.17540.2048-0.10870.0383-0.121-0.08530.21290.0603-0.15870.12830.00010.37380.0155-0.00530.3678-0.04970.4292-8.0004-63.3228-16.272
70.0528-0.07240.02650.1943-0.38820.5442-0.1189-0.2056-0.23210.14980.05890.0833-0.00360.0878-0.00070.48720.07650.00170.47920.00590.3429-6.8457-35.32872.1397
81.35240.26611.23972.72720.73380.7723-0.1784-0.0529-0.37530.35350.47610.24920.23780.5570.11910.47770.0990.07540.3714-0.03670.3824-5.6333-74.0643-12.3498
90.03190.1480.1990.3726-0.12631.2988-0.03920.1137-0.08260.6948-0.31750.04210.10310.1445-0.01170.42650.01390.02030.30480.07360.4133-11.1406-63.6235-8.0561
100.19280.2494-0.12480.6032-0.7861.06020.3017-0.4666-0.57880.0420.07250.13721.3028-1.06570.08090.4088-0.0685-0.03220.69670.08170.5021-29.9148-25.5259-14.8859
110.11920.18660.20650.39940.01370.36450.1848-0.1665-0.00650.3847-0.5038-0.1719-0.3401-0.7949-0.00710.46380.11860.01590.5984-0.02880.5352-30.1023-16.3512-15.6861
121.4641.3289-0.24150.90010.38220.8505-0.18870.2507-0.1657-0.01180.20970.07630.3974-0.5342-0.05510.4110.0079-0.05520.58420.01350.4272-24.3547-22.2708-29.0583
130.92350.30950.28130.304-0.2520.2636-0.0668-0.0396-0.13550.1516-0.1460.1619-0.2431-0.56130.00010.4-0.00790.00260.37250.01810.3595-22.2998-20.0691-14.132
142.4192-0.3592.96341.4811-0.56263.9498-0.05490.42740.11120.1012-0.2575-0.42640.44251.0915-0.34870.2677-0.03720.00080.30720.04670.3831-11.9793-17.8264-30.5662
151.63950.7753-0.69640.4448-0.11960.38060.2055-0.32230.37470.22870.0394-0.21690.1989-0.68670.00220.46790.0486-0.09230.415-0.00080.4604-15.3696-12.246-22.8601
163.52231.21474.66645.02862.19337.2667-0.48590.21710.0458-0.18010.2248-0.2781-0.28821.53460.98610.4306-0.0156-0.0720.51370.03440.3787-11.0928-19.8415-11.0953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 77 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 88 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 123 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 133 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 48 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 77 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 93 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 116 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 133 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 43 through 58 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 59 through 71 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 72 through 93 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 94 through 117 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 118 through 135 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 136 through 152 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 153 through 164 )C0

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