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- PDB-5bq8: Crystal structure of Norrin, a Wnt signalling activator, Crystal ... -

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Basic information

Entry
Database: PDB / ID: 5bq8
TitleCrystal structure of Norrin, a Wnt signalling activator, Crystal Form II
Components(Norrin) x 3
KeywordsSIGNALING PROTEIN / Wnt signalling pathway / Norrie disease protein / cystine-knot like growth factor / ligand for Frizzled 4 receptor
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / ubiquitin-dependent endocytosis / retina layer formation / retinal pigment epithelium development ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / ubiquitin-dependent endocytosis / retina layer formation / retinal pigment epithelium development / establishment of blood-retinal barrier / microglial cell proliferation / glycine metabolic process / endothelial cell differentiation / dendritic spine development / establishment of blood-brain barrier / protein targeting to lysosome / vacuole organization / microglia differentiation / frizzled binding / optic nerve development / retinal ganglion cell axon guidance / lens development in camera-type eye / exploration behavior / action potential / smoothened signaling pathway / decidualization / canonical Wnt signaling pathway / response to axon injury / blood vessel remodeling / glutathione metabolic process / tricarboxylic acid cycle / visual perception / transforming growth factor beta receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytokine activity / mitotic cell cycle / nervous system development / cellular response to hypoxia / angiogenesis / neuron apoptotic process / collagen-containing extracellular matrix / transcription by RNA polymerase II / protein ubiquitination / inflammatory response / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space
Similarity search - Function
Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / 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 ...Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Norrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 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 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Norrin
D: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9698
Polymers54,7564
Non-polymers2124
Water2,198122
1
A: Norrin
B: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4003
Polymers27,3652
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-29 kcal/mol
Surface area11900 Å2
MethodPISA
2
C: Norrin
D: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5695
Polymers27,3922
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-33 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.667, 53.059, 96.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 3 types, 4 molecules ACBD

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


Mass: 13668.798 Da / Num. of mol.: 2 / Fragment: UNP residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): 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: 13695.845 Da / Num. of mol.: 1 / Fragment: UNP residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604
#3: Protein Norrin / / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 13722.891 Da / Num. of mol.: 1 / Fragment: UNP residues 25-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604

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Non-polymers , 3 types, 126 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 sodium acetate, pH 5.0, 5% PGA-LM, 4% PEG2000MME, 24% PEG550MME

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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→33.65 Å / Num. obs: 36272 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.289 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPU

5bpu


Resolution: 2→33.65 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1801 4.98 %Random selection
Rwork0.233 ---
obs0.2338 36194 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 10 122 3319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053278
X-RAY DIFFRACTIONf_angle_d1.0764365
X-RAY DIFFRACTIONf_dihedral_angle_d13.9231265
X-RAY DIFFRACTIONf_chiral_restr0.042472
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05411332598X-RAY DIFFRACTION100
2.0541-2.11451502589X-RAY DIFFRACTION100
2.1145-2.18270.35721180.33912611X-RAY DIFFRACTION100
2.1827-2.26071522589X-RAY DIFFRACTION100
2.2607-2.35120.31451270.28182644X-RAY DIFFRACTION100
2.3512-2.45820.30291380.28692595X-RAY DIFFRACTION100
2.4582-2.58780.28061450.26492631X-RAY DIFFRACTION100
2.5878-2.74980.26511330.25312633X-RAY DIFFRACTION100
2.7498-2.9620.28521420.25512632X-RAY DIFFRACTION100
2.962-3.25990.221510.222644X-RAY DIFFRACTION100
3.2599-3.73110.24741400.20522665X-RAY DIFFRACTION100
3.7311-4.69870.21051420.17682699X-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)
10.95640.584-0.09170.14830.2990.59840.1515-0.3081-0.05940.0552-0.13080.03490.1659-0.0361-0.00170.3922-0.02590.04310.50660.08520.387-15.948914.4495-10.6795
20.6933-0.30990.09490.6512-0.08090.60860.0461-0.43120.01210.04870.031-0.0940.06560.04910.01890.38680.024-0.01820.44780.05020.30747.830314.4056-10.2958
30.7336-0.45440.10170.46360.10590.9024-0.08550.40550.1289-0.11290.04340.02840.09-0.1298-0.00040.3549-0.0422-0.03090.40610.04030.3429-10.741616.5304-38.0973
41.0902-0.4482-0.46940.67910.1390.7916-0.03330.2548-0.1566-0.10090.0826-0.10740.12980.02580.01570.3527-0.00780.04010.337-0.02140.326812.653612.0767-37.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 35 through 138)
2X-RAY DIFFRACTION2(chain 'B' and resid 36 through 132)
3X-RAY DIFFRACTION3(chain 'C' and resid 35 through 133)
4X-RAY DIFFRACTION4(chain 'D' and resid 37 through 138)

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