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

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Basic information

Entry
Database: PDB / ID: 5bpu
TitleCrystal structure of Norrin, a Wnt signalling activator, Crystal Form I
Components
  • (GGL)EEE
  • (GGL)EEEEEE
  • Norrin
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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_validate_polymer_linkage
Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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
E: Norrin
F: Norrin
H: (GGL)EEEEEE
I: (GGL)EEE


Theoretical massNumber of molelcules
Total (without water)83,1458
Polymers83,1458
Non-polymers00
Water2,954164
1
A: Norrin
B: Norrin
H: (GGL)EEEEEE


Theoretical massNumber of molelcules
Total (without water)28,1513
Polymers28,1513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Norrin
D: Norrin
H: (GGL)EEEEEE
I: (GGL)EEE


Theoretical massNumber of molelcules
Total (without water)28,6864
Polymers28,6864
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Norrin
F: Norrin
I: (GGL)EEE


Theoretical massNumber of molelcules
Total (without water)27,7643
Polymers27,7643
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.370, 79.100, 234.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13614.706 Da / Num. of mol.: 6 / 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/peptide (GGL)EEEEEE


Mass: 921.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide (GGL)EEE


Mass: 534.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, pH 5.0, 5% PGA-LM, 30% PEG550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionRedundancy: 33.3 % / Number: 499350 / Rmerge(I) obs: 0.167 / D res high: 3.18 Å / D res low: 116.39 Å / Num. obs: 14982 / % possible obs: 99.9 / Rejects: 4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
3.183.2610.7489.9
14.22116.3910.08327.7
ReflectionResolution: 2.4→65.56 Å / Num. obs: 34791 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.95 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.061 / Net I/σ(I): 7.8 / Num. measured all: 194342 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obs
2.4-2.495.71.92054135810.3510.423100
8.98-65.56520.539367880.9950.0299.80.039

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.1.29data scaling
PHENIXphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→65.559 Å / FOM work R set: 0.7181 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 1745 5.03 %
Rwork0.2166 32944 -
obs0.2189 34689 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.99 Å2 / Biso mean: 70 Å2 / Biso min: 24.93 Å2
Refinement stepCycle: final / Resolution: 2.4→65.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 101 164 5094
Biso mean--91.51 55.17 -
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045069
X-RAY DIFFRACTIONf_angle_d0.9326751
X-RAY DIFFRACTIONf_chiral_restr0.039731
X-RAY DIFFRACTIONf_plane_restr0.004865
X-RAY DIFFRACTIONf_dihedral_angle_d16.3122047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.40881400.352700X-RAY DIFFRACTION100
2.4706-2.55040.35941500.33312699X-RAY DIFFRACTION100
2.5504-2.64150.34421310.29742685X-RAY DIFFRACTION100
2.6415-2.74730.32351470.28582711X-RAY DIFFRACTION100
2.7473-2.87230.31691470.27812711X-RAY DIFFRACTION100
2.8723-3.02380.38031330.26932717X-RAY DIFFRACTION100
3.0238-3.21320.29841430.24782728X-RAY DIFFRACTION100
3.2132-3.46130.2761490.22992733X-RAY DIFFRACTION100
3.4613-3.80960.25851470.20782762X-RAY DIFFRACTION99
3.8096-4.36080.23351480.17082748X-RAY DIFFRACTION100
4.3608-5.49370.18251600.14772790X-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)
10.3797-0.52230.93791.4837-0.73511.6466-0.07620.6461-0.69120.2656-0.9442-0.1467-0.5118-1.8703-0.25730.3913-0.31710.12660.39110.01640.4019-4.9092-4.8602-0.912
20.0513-0.2370.14070.27610.20380.2891-0.0684-0.09460.0497-0.02020.1029-0.05790.0516-0.19550.02840.3021-0.0014-0.07380.20640.09020.37973.932316.0318-0.6098
30.0637-0.09370.01710.0180.012-0.0503-0.54620.13850.13770.56620.5406-0.4838-0.50330.04470.02080.3586-0.0081-0.11380.54150.17110.567323.37352.061529.4545
40.1546-0.1117-0.3758-0.23280.71141.1205-0.102-0.10130.0755-0.1689-0.1055-0.41560.14110.0086-0.00440.3203-0.0167-0.07880.24670.05310.405511.044915.3503-3.2627
50.1558-0.10440.03530.0341-0.10870.00910.51590.2646-0.4506-0.0928-0.3394-0.7394-0.12810.2590.0010.71530.05320.0010.80130.03430.641423.217911.33743.4599
60.52970.13-0.54850.7534-0.58760.7146-0.2185-0.159-0.0053-0.32660.1646-0.20390.3281-0.4547-0.07780.30130.0041-0.09420.19770.06190.403910.6762-4.271223.5768
70.17-0.00090.16480.1331-0.13810.08720.0402-0.17790.21840.3561-0.0597-0.0945-0.55080.11650.1650.4813-0.0132-0.1630.25130.06250.53612.649620.24320.4613
81.44780.3565-0.31890.16960.27770.4968-0.1847-0.7681-0.1632-0.0130.28560.15120.0524-0.4809-0.06510.36830.0241-0.05160.4950.0920.269617.5092-2.127834.0683
9-0.07460.04230.15320.04850.1070.17910.21390.02270.18130.21850.20080.1338-1.1846-0.17010.00090.5561-0.0055-0.03840.4647-0.03530.36216.87418.417520.9561
100.94660.78530.27920.62060.21190.0913-0.4634-0.9872-0.03240.6888-0.12750.9310.09040.0281-0.47690.31970.07550.1740.78120.09630.5923-7.94481.7566-29.5222
110.02290.03180.0346-0.04310.05860.13830.0445-0.40260.4234-0.744-0.02950.3331-0.1122-0.35120.00070.5568-0.0532-0.07920.47440.1530.58366.13897.9398-38.831
120.20730.03180.27040.29690.13240.1752-0.1435-0.55230.4549-0.1887-0.40140.3703-0.5902-0.4971-0.06680.6473-0.16760.0490.22650.4840.078816.975711.0413-41.4053
130.05680.0531-0.18290.059-0.26670.01230.19480.2575-0.105-0.4958-0.1205-0.20160.8275-0.3923-0.00020.5270.0060.03250.42020.07310.41690.439-7.8084-18.2167
140.1815-0.1807-0.01460.064-0.0325-0.047-0.518-0.2015-0.43790.5675-0.6487-0.53740.19370.8556-0.00070.68720.03130.05410.44580.13490.64614.4006-20.9111-7.9024
150.0567-0.12230.00390.06190.09630.1135-0.5546-0.16930.0724-0.50810.4614-0.47010.22430.00460.00840.3531-0.10040.06060.41630.06580.3916.3638-12.9205-15.3083
160.4746-0.1390.21680.4990.3760.31250.1131-0.1052-0.1977-0.38020.2684-0.11290.00840.50860.01570.4788-0.11420.06290.5402-0.06860.31910.4983-1.6807-39.7339
170.03780.027-0.0220.06240.04920.0287-0.05341.4780.4262-0.75020.58930.2971-0.2792-0.4481-0.00010.8593-0.3790.13351.58420.18161.259827.232313.3251-51.937
180.62740.1841-0.18510.2823-0.01380.05970.21940.30871.3124-0.5754-0.1505-0.1062-0.19250.0316-0.00370.6451-0.09840.13680.57520.02310.450215.41182.0597-44.0233
190.2561-0.1348-0.28720.16850.05510.13560.44390.2775-0.043-0.12430.40680.2860.50460.4930.00050.526-0.02640.00430.62610.02840.34036.3206-8.1221-30.5116
200.0574-0.0107-0.09520.0497-0.00870.09310.1235-0.28550.662-0.94710.26660.12160.6576-0.4894-0.00010.5394-0.1356-0.03160.5490.06940.7262-5.50722.3604-11.0074
210.3052-0.6403-0.07410.5953-0.1558-0.1625-0.249-0.1577-0.46490.21110.4710.81930.0746-0.3820.01740.5703-0.03080.01710.24210.09520.61411.6979-20.8933-3.7773
220.6365-0.083-0.13090.1187-0.46020.62010.6113-0.07240.2615-0.05760.19590.0244-0.59940.35840.18770.3460.020.04420.49870.0860.37284.50862.0226-24.3091
23-0.04560.120.08240.65420.68620.33930.0746-0.56470.38780.12510.4728-0.20620.18470.7560.01180.304-0.0353-0.05030.44640.0590.520118.21160.022-35.7464
240.4103-0.5917-0.32550.68090.33420.0876-0.07660.0587-0.1590.4299-0.0103-0.105-0.21540.17490.02790.4815-0.0191-0.08650.28390.09760.41789.3031-14.986-4.2878
251.0402-0.37260.46120.52130.30531.5379-0.0625-0.07280.0843-0.1265-0.15790.1358-0.20.1466-0.05020.36120.06340.12110.46070.07970.453-19.8765-9.8101-34.3442
260.0179-0.1619-0.48970.4198-0.85080.77720.14280.1372-0.19490.385-0.111-0.08150.36060.14150.00670.41180.02710.08920.50220.03480.5124-3.7429-11.8319-62.6436
270.761-0.43990.61350.5680.73661.30160.1668-0.0796-0.24130.2574-0.0346-0.18060.02670.16280.41690.2641-0.02260.02220.390.12070.3283-13.6352-16.9295-35.6831
280.270.0703-0.21050.09370.19970.26990.1418-0.18510.56790.32560.2794-0.43-0.70340.3480.01980.68450.18850.19580.53670.15370.4895-3.7705-0.1334-68.0989
290.0651-0.0345-0.05690.02410.03240.01450.02820.3621-0.1202-0.0541-0.75410.05450.29520.4833-0.00041.05020.31080.05221.0193-0.09410.825212.0437-20.1464-75.7691
300.1597-0.270.06550.199-0.1330.13280.047-0.3155-0.24540.08890.0251-0.2120.21780.57060.00020.47810.02150.09540.6163-0.00820.290.2345-5.738-72.9196
310.1374-0.2423-0.36070.2155-0.36090.25940.2179-0.01580.2206-0.08970.0887-0.0274-0.2193-0.38250.07370.3560.09920.10090.45330.02170.3324-14.1197-4.1108-49.2596
32-0.06340.0817-0.05160.0376-0.0512-0.04330.0743-0.85980.3370.77690.1114-0.06780.3647-0.192-0.00010.4601-0.08840.06770.51420.07970.6924-18.0872-24.0509-38.9874
330.05070.16120.01160.9330.04440.01420.01980.1520.3237-0.12860.050.86470.3506-0.21280.03220.3547-0.02250.16190.7147-0.01350.5041-15.6924-11.7337-46.4081
340.6660.20580.45560.11620.0240.2965-0.16260.3130.0618-0.19810.01740.27680.18770.1697-0.04850.4210.09860.0090.83540.06910.3517-6.1105-11.8319-72.6402
350.05790.04660.02940.03880.04290.02810.46810.1756-0.0505-0.24720.42050.12570.1023-0.17770.00171.0880.57070.07791.30960.12431.340511.5114-25.1837-83.0847
360.78330.16750.14980.19090.24980.6545-0.34980.8986-0.5498-1.62630.3694-0.17580.5456-1.0075-0.05340.9584-0.06610.28950.8341-0.2160.6016-1.7018-15.9903-77.2746
370.13710.24360.393.91570.69832.38731.13411.0359-0.16361.5631.02590.8411.4395-0.4940.3410.3257-0.00950.05680.93920.00380.3533-13.8781-8.2085-61.5511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 77 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 88 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 130 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 141 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 77 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 93 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 123 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 133 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 33 through 39 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 40 through 48 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 49 through 66 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 67 through 77 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 78 through 88 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 89 through 93 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 94 through 108 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 109 through 115 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 116 through 123 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 124 through 135 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 32 through 39 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 40 through 66 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 67 through 77 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 78 through 93 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 94 through 133 )D0
25X-RAY DIFFRACTION25chain 'E' and (resid 34 through 66 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 67 through 93 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 94 through 133 )E0
28X-RAY DIFFRACTION28chain 'F' and (resid 35 through 48 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 49 through 57 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 58 through 66 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 67 through 77 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 78 through 88 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 89 through 93 )F0
34X-RAY DIFFRACTION34chain 'F' and (resid 94 through 109 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 110 through 114 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 115 through 123 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 124 through 133 )F0

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