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

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Basic information

Entry
Database: PDB / ID: 5bqb
TitleCrystal structure of Norrin, a Wnt signalling activator, Crystal Form III
ComponentsNorrin
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 / protein targeting to lysosome / establishment of blood-brain barrier / 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 / collagen-containing extracellular matrix / angiogenesis / neuron apoptotic process / 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
CITRIC ACID / Norrin
Similarity search - Component
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 1.4Jan 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)55,29810
Polymers54,4594
Non-polymers8396
Water1,29772
1
A: Norrin
B: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6495
Polymers27,2292
Non-polymers4203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-34 kcal/mol
Surface area12820 Å2
MethodPISA
2
C: Norrin
D: Norrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6495
Polymers27,2292
Non-polymers4203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-29 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.761, 38.095, 177.197
Angle α, β, γ (deg.)90.000, 93.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13614.706 Da / Num. of mol.: 4 / 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 / Production host: Homo sapiens (human) / References: UniProt: Q00604
#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M citrate, pH 5.0, 30% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→44.19 Å / Num. obs: 26073 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 51.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Net I/σ(I): 16.7 / Num. measured all: 151301
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3860.821531525380.7210.3697.7
8.91-44.195.10.03152.425224960.9980.01598

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å44.19 Å
Translation2.3 Å44.19 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.2.17data scaling
Cootmodel building
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPU

5bpu


Resolution: 2.3→44.19 Å / FOM work R set: 0.6505 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1354 5.19 %Random selection
Rwork0.2212 24717 --
obs0.2228 26071 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 283.09 Å2 / Biso mean: 91.3 Å2 / Biso min: 24.76 Å2
Refinement stepCycle: final / Resolution: 2.3→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 54 72 3230
Biso mean--142.13 71.59 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043246
X-RAY DIFFRACTIONf_angle_d0.9154324
X-RAY DIFFRACTIONf_chiral_restr0.034462
X-RAY DIFFRACTIONf_plane_restr0.004550
X-RAY DIFFRACTIONf_dihedral_angle_d21.1151254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.38231190.30642458X-RAY DIFFRACTION98
2.3822-2.47760.29791340.29142448X-RAY DIFFRACTION100
2.4776-2.59030.32781270.2742378X-RAY DIFFRACTION98
2.5903-2.72690.32091450.26882452X-RAY DIFFRACTION99
2.7269-2.89770.26921410.25912468X-RAY DIFFRACTION100
2.8977-3.12140.28381260.24382486X-RAY DIFFRACTION99
3.1214-3.43540.28751340.23212459X-RAY DIFFRACTION99
3.4354-3.93220.23611320.20882489X-RAY DIFFRACTION99
3.9322-4.95310.20091420.172488X-RAY DIFFRACTION100
4.9531-44.20.23441540.22152591X-RAY DIFFRACTION99
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)
16.61054.53715.00463.20613.36653.8045-0.01190.61151.17730.524-0.11640.5582-0.3826-1.8036-4.18290.80250.23810.23680.7753-0.0660.744410.8982.883420.93
20.45190.4113-0.02222.0971-1.33010.33850.09990.1860.25790.1610.0354-0.335-0.31670.02440.01020.34610.0195-0.01980.24210.01590.447226.9681-3.69574.9765
30.8275-0.3762-0.23410.1337-0.08340.06240.2145-0.28480.16210.178-0.07220.1256-0.3834-0.1327-0.00080.5401-0.10690.07480.52770.01610.451513.2292-8.998132.1193
41.99491.6907-1.43072.4632-2.99085.27230.38130.3156-0.7888-1.5716-0.23690.78872.58581.1355-0.13220.7530.0396-0.03660.8273-0.03140.583219.7474-28.163840.7015
50.41131.00190.09761.5254-0.65442.06050.00790.2180.0414-0.03150.16030.0754-0.1513-0.36690.01770.26880.00480.00350.23160.01470.331322.6266-12.00447.4435
60.09770.17-0.01690.04490.06550.22570.4212-0.28690.14951.2583-0.46230.5815-0.48960.0813-0.00070.50.0135-0.01160.5065-0.03280.442813.0492-12.027819.2346
70.5735-0.2559-0.01160.09210.05490.50160.2491-0.4360.4795-0.6271-0.09570.6088-0.3071-0.07180.00150.8497-0.08060.14170.6839-0.05250.61913.8018-9.590244.4177
81.4639-0.3208-0.10940.0920.11690.014-0.24850.1282-0.244-0.27330.59221.0784-0.1153-0.33140.00920.5777-0.17890.04550.72740.04380.706210.192-24.754848.1899
91.98841.1082-0.74630.7818-0.87151.87180.10890.0999-0.09660.2259-0.0544-0.18980.7410.35040.13190.3641-0.0029-0.0270.29920.00750.405523.762-10.348715.8208
101.3407-1.04660.90850.762-0.56980.6580.2348-0.4728-0.3019-0.1848-0.17220.2273-0.0160.3181-0.00010.4494-0.209-0.04630.67090.00580.499518.7577-24.076347.3938
110.15070.17780.00260.0668-0.2080.20010.6964-0.08320.33910.2461-0.353-0.06420.10420.06520.00050.7939-0.1521-0.05270.6387-0.07180.480824.3955-11.201333.7121
121.9959-3.6102-1.56256.90064.4898.76540.1238-0.5094-0.79640.2235-0.01682.3410.0999-1.0518-0.67670.8733-0.1590.42721.11980.27411.07320.0691-6.138364.0527
130.6093-1.2651-0.13521.87550.0080.14-0.3562-0.39870.5686-0.0542-0.1977-0.27410.31080.1881-0.00010.487-0.1687-0.05880.83560.10.758533.01698.870951.0438
140.85841.1209-0.70541.3567-0.79860.85780.0416-0.2482-0.32730.2785-0.2420.56570.32040.16120.00041.15680.0178-0.02630.99690.02920.496740.8719-21.048270.3058
151.0697-0.10380.85341.37440.29010.567-0.30330.49760.0701-0.64810.3658-0.18870.3993-0.55140.00040.6252-0.218-0.01570.870.06490.535435.95873.141645.3991
162.2439-1.3331-0.99835.195-0.05781.7596-0.04050.19050.18010.19030.81380.83481.660.98-0.15390.7201-0.0272-0.16070.9342-0.0480.256132.0595-12.025857.7411
170.51980.3576-0.25040.2295-0.08320.0023-0.1739-0.2283-0.55411.398-0.29550.7071-0.490.0458-0.00031.57860.13060.05971.541-0.00070.777633.567-19.712481.6592
180.0544-0.0590.02670.0117-0.02820.0148-0.8806-0.10890.51490.12-1.0731-0.2687-0.48820.1865-0.00512.05730.0964-0.14731.4348-0.0411.774647.7796-40.490676.1072
190.5250.115-0.02670.589-1.49431.8051-0.5832-1.11540.62791.850.92520.4651-1.19-0.34750.19651.23580.2757-0.14981.198-0.01440.301434.615-13.333172.8804
200.0278-0.0856-0.26660.59941.11412.8429-0.53060.11321.032-0.06170.3942-0.84070.82930.47580.07790.5831-0.1530.07980.6311-0.01241.036342.95770.913147.2487
210.12010.078-0.02840.0720.02170.0747-0.2435-0.18060.24010.96310.1727-0.7114-0.99470.8377-0.00190.8595-0.1281-0.35540.84650.06950.781137.1735-2.756559.7378
220.62190.278-0.55390.1648-0.27270.3496-0.38430.09610.24280.37780.3664-0.7356-1.06310.5284-0.01031.07950.255-0.30571.0699-0.2040.71846.6939-22.628579.5189
230.0005-0.138-0.05870.09690.11140.1412-0.34310.1377-1.13640.8569-0.1866-1.34260.15120.05340.00051.10540.1888-0.07661.62680.2881.55451.9691-31.917980.2211
241.03880.0126-0.22360.6306-0.67930.8224-0.11320.83460.91221.2111-0.3752-0.48310.11530.53080.23351.39310.0783-0.28351.2590.0620.5640.946-9.81473.3779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 66 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 77 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 88 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 123 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 133 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 48 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 66 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 93 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 123 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 133 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 39 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 40 through 66 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 67 through 93 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 94 through 123 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 124 through 133 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 36 through 47 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 48 through 58 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 59 through 77 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 78 through 88 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 89 through 93 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 94 through 110 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 111 through 123 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 124 through 133 )D0

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