Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan
- University of Oxford, United Kingdom
Figures
Figure 1
Expression and purification of biologically active recombinant Norrin.
(A) Schematic diagrams of the expression constructs including Norrin (a signal peptide, SP, followed by Norrin and Rho-1D4 tag at C-terminus) and SUMO-Norrin (a SP followed by a Strep-tag II, an …
Figure 2 with 3 supplements
Crystal structure and structural analysis of apo Norrin.
(A) Schematic diagram of Norrin is rainbow coloured and disulphide bonds are drawn as lines. Cartoon representation of dimeric Norrin. Four intramolecular disulphide bonds are shown as magenta …
Figure 2—figure supplement 1
Electron density map of Norrin structure.
The initial density modified map from PHENIX AUTOSOL (Terwilliger, 2000, Terwilliger et al., 2009) calculated with experimental Se-Met SAD phases is contoured at 1.5 σ and shown as blue meshes. The …
Figure 2—figure supplement 2
Multiple sequence alignment of Norrin.
Secondary structure element colouring corresponds to Figure 2A. The magenta boxes represent conserved cysteine residues in the cystine-knot growth factor superfamily, whereas the yellow boxes denote …
Figure 2—figure supplement 3
Norrin solution structure and structural analyses.
(A) SAXS analysis of Norrin. The experimental scattering data (black circles) and calculated scattering pattern (green line) are shown and the Norrin solution structure model is shown in cartoon …
Figure 3 with 2 supplements
Crystal and solution structures of unliganded Fz4CRD.
(A) Schematic domain organization (SP, signal peptide; TM. transmembrane domain; CD, cytoplasmic domain). Crystallization constructs are rainbow coloured. Disulphide bonds are drawn and blue …
Figure 3—figure supplement 1
Multiple sequence alignment and structural analysis of cysteine-rich like domains.
(A) Secondary structure assignment colouring corresponds to Figure 3A. The conserved cysteine residues (highlighted in cyan) form five disulphide bridges, drawn in black lines and labelled as I–V. …
Figure 3—figure supplement 2
Distinct dimeric assembly of Fz4CRD and mouse Fz8CRD observed from crystal structures.
(A) The superimposition of Fz4CRD structures from two crystal forms, coloured as pink and magenta for crystal form I and green and gray for crystal form II. (B) The structure of dimeric mouse Fz8CRD …
Figure 4 with 4 supplements
Crystal structure and solution behaviour of Norrin–Fz4CRD complex.
(A) Ribbon representation of Norrin (magenta and pink) in a 2:2:2 complex with Fz4CRD (cyan and pale cyan) and SOS (green). (B) SEC-MALS analyses. The profile of molecular weight (left ordinate …
Figure 4—figure supplement 1
Protein complex production and structural properties of Norrin–Fz4CRD complex.
(A) Norrin forms a stable complex with Fz4CRD in solution. SEC elution profiles and SDS-PAGE under reducing condition are presented. SEC fractions analysed by SDS-PAGE are marked as red lines for …
Figure 4—figure supplement 2
Structural comparison of cystine-knot growth factor monomers and their ternary complexes.
Norrin has a unique three intermolecular disulphide bonds arrangement and a specific intramolecular disulphide bond (black dotted circle). (A) Cartoon representation of a single chain of …
Figure 4—figure supplement 3
No large conformational changes upon complex formation.
(A) Structural comparisons Fz4CRD (gray) from Norrin–Fz4CRD–SOS complex with Fz4CRD (cyan) from methylated Norrin–Fz4CRD and unliganded Fz4CRD (magenta) crystal form II (chain D) are presented as a …
Figure 4—figure supplement 4
Structural comparison of Norrin–Fz4CRD complex with MBP-Norrin.
(A) Superposition of MBP-Norrin (green; PDB ID: 4MY2) onto Norrin in the Norrin (magenta)–Fz4CRD (blue)–SOS (wheat) and methylated Norrin (yellow)–Fz4CRD (cyan) complex structures. (B) Close-up view …
Figure 5
Structural details of binding sites in the Norrin–Fz4CRD–SOS complex.
(A) Side-view of complex. Fz4CRD loops involved in Norrin binding are coloured blue (loop I), green (loop II), and yellow (loop III). (B–E) Views detailing the interfaces. Selected residues involved …
Figure 6 with 1 supplement
Biophysical and functional characterisation of Fz4 binding site.
Surface representation of Norrin–Fz4CRD complex in open book view. (A) Interface residues are coloured orange (Norrin) and blue (loop I), green (loop II), yellow (loop III), and cyan (Phe96) on Fz4CR…
Figure 6—figure supplement 1
SPR equilibrium binding data.
SPR equilibrium binding experiments using Fz4CRD as analyte and biotinylated human Norrin wild-type (WT) and mutants as immobilized ligands on CM5 sensor chips. SPR sensorgrams (left panels) and …
Figure 7 with 1 supplement
Verification of Norrin GAG binding site.
Heparin affinity chromatography of (A) Norrin–Fz4CRD complex and (B) Norrin R107E/R109E/R115L–Fz4CRD complex. Protein elution profiles (left panel) were monitored by absorbance at 280 nm (blue …
Figure 7—figure supplement 1
Supporting experiments for GAG binding site.
(A) Heparin affinity chromatography of Norrin wild-type. Protein elution profiles (left panel) were monitored by absorbance at 280 nm (blue curves) for a NaCl gradient (0.25–2 M; black dashed …
Figure 8 with 1 supplement
The potential Lrp5/6 binding site on Norrin.
(A) Cartoon representation of Norrin (grey) in complex with Fz4CRD (cyan). Residues in the potential Lrp5/6 binding site are shown as spheres (atom colouring: magenta, carbon; blue, nitrogen; red, …
Figure 8—figure supplement 1
Verification of Norrin potential Lrp5/6 binding site.
(A) Luciferase reporter assay. The luciferase activities were normalized to a maximum activity value (100%) for Norrin wild-type and error bars represent standard deviations (n = 3). (B) SPR binding …
Figure 9
Structural comparison of Norrin–Fz4CRD with Wnt8–Fz8CRD.
(A) Superposition of Norrin (magenta)–Fz4CRD (cyan) with Wnt8 (green)–Fz8CRD (blue) (PDB ID: 4F0A). Disulphide bonds, N-linked glycans, and PAM (of Wnt8) are shown as sticks. SOS is shown as grey …
Tables
Table 1
Data collection, phasing and refinement statistics
| Norrin–Fz4CRD–SOS | Methylated Norrin–Fz4CRD | Norrin | Norrin Se-Met | Methylated Norrin | |
|---|---|---|---|---|---|
| Crystal form | I | I | II | ||
| Data collection | |||||
| Space group | P6122 | P4322 | P212121 | P212121 | P212121 |
| Cell dimensions | |||||
| a, b, c (Å) | 119.1, 119.1, 119.2 | 98.9, 98.9, 120.4 | 46.4, 79.1, 243.3 | 45.8, 78.8, 232.8 | 102.7, 53.1, 96.1 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 120 | 90, 90, 90 | 90, 90, 90 | 90, 90, 90 |
| Peak | |||||
| Wavelength | 0.9200 | 0.9795 | 0.9686 | 0.9795 | 0.9795 |
| Resolution (Å) | 47.34–3.00 (3.18– 3.00) | 49.46–2.30 (2.38–2.30) | 65.56–2.40 (2.49–2.40) | 116.39–3.18 (3.26–3.18) | 33.65–2.00 (2.05–2.00) |
| Rpim (%) | 3.1 (54.8) | 4.5 (56.1) | 6.1 (42.3) | 2.8 (23.4) | 4.1 (58.3) |
| I/σI | 14.6 (1.6) | 10.7 (1.4) | 7.8 (1.9) | 20.2 (3.0) | 9.1 (1.7) |
| Completeness (%) | 100 (100) | 98.9 (97.2) | 99.9 (100) | 99.9 (99.9) | 100 (100) |
| Redundancy | 19.6 (20.6) | 6.0 (5.6) | 5.6 (5.7) | 33.3 (9.9) | 5.6 (5.8) |
| Refinement | |||||
| Resolution (Å) | 47.34–3.00 (3.18–3.00) | 49.46–2.30 (2.38–2.30) | 65.56–2.40 (2.49–2.40) | 33.65–2.00 (2.05–2.00) | |
| No. reflections | 10,503 (1648) | 26,816 (2514) | 34,722 (3384) | 36,272 (2635) | |
| Rwork/Rfree | 21.5/26.7 | 19.7/22.1 | 21.6/26.2 | 23.3/24.8 | |
| No. atoms | |||||
| Protein | 1759 | 2557 | 4930 | 3187 | |
| Ligand/ion | 83 | 39 | 101 | 10 | |
| Water | 0 | 115 | 164 | 122 | |
| B-factors | |||||
| Protein | 113 | 63 | 70 | 57 | |
| Ligand/ion | 133 | 71 | 92 | 73 | |
| Water | 0 | 57 | 55 | 51 | |
| R.m.s deviations | |||||
| Bond lengths (Å) | 0.005 | 0.004 | 0.009 | 0.005 | |
| Bond angles (°) | 1.18 | 0.93 | 1.08 | 1.07 | |
| Ramachandran plot | |||||
| Favored (%) | 95.5 | 97.0 | 96.7 | 97.2 | |
| Allowed (%) | 4.5 | 3.0 | 3.3 | 2.8 | |
| PDB code | 5BQC | 5BQE | 5BPU | 5BQ8 | |
| Norrin | Fz4CRD | Fz4CRD | |
|---|---|---|---|
| Crystal form | III | I | II |
| Data collection | |||
| Space group | C121 | P212121 | P61 |
| Cell dimensions | |||
| a, b, c (Å) | 86.8, 38.1, 177.2 | 72.6, 102.1, 116.5 | 76.1, 76.1, 204.5 |
| α, β, γ (°) | 90, 94, 90 | 90, 90, 90 | 90, 90, 90 |
| Wavelength | 0.9795 | 0.9686 | 0.9686 |
| Resolution (Å) | 44.19–2.30 (2.38–2.30) | 41.77–2.20 (2.27–2.20) | 47.37–2.40 (2.49–2.40) |
| Rpim (%) | 2.8 (36) | 4.1 (49.5) | 2.6 (33.9) |
| I/σI | 16.7 (2.0) | 12.8 (2.0) | 14.5 (2.2) |
| Completeness (%) | 99.2 (97.7) | 99.2 (99.7) | 99.5 (99.4) |
| Redundancy | 5.8 (6.0) | 4.3 (4.4) | 4.0 (4.1) |
| Refinement | |||
| Resolution (Å) | 44.19–2.30 (2.38–2.30) | 41.77–2.20 (2.27–2.20) | 47.37–2.40 (2.49–2.40) |
| No. reflections | 26,073 (2538) | 44,268 (3802) | 25,975 (2724) |
| Rwork/Rfree | 22.1/25.0 | 17.7/22.3 | 20.3/24.3 |
| No. atoms | |||
| Protein | 3104 | 3866 | 3877 |
| Ligand/ion | 72 | 70 | 99 |
| Water | 54 | 148 | 69 |
| B-factors | |||
| Protein | 91 | 47 | 76 |
| Ligand/ion | 72 | 67 | 72 |
| Water | 142 | 43 | 68 |
| R.m.s deviations | |||
| Bond lengths (Å) | 0.006 | 0.01 | 0.005 |
| Bond angles (°) | 1.03 | 1.35 | 0.94 |
| Ramachandran plot | |||
| Favored (%) | 96.0 | 99.0 | 97.0 |
| Allowed (%) | 4.0 | 1.0 | 3.0 |
| PDB code | 5BQB | 5BPB | 5BPQ |
-
All structures were determined from one crystal.
-
Values in parentheses are for highest-resolution shell.
Table 2
Molecular properties of the proteins determined by SAXS
| Proteins | N-Glyc state | Rg (nm)* | Dmax (nm)† | Volume porod (Vp [nm3]) | MWTheoretical (kDa)‡ | MWMeasured (KDa)§ | MWMeasured (KDa)# |
|---|---|---|---|---|---|---|---|
| Fz4CRD | deglyc¶ | 1.98 | 6.93 | 33.0 | 17.1 (monomer) | 15.9 | 19.9 |
| Fz4CRD | glyc** | 2.24 | 7.84 | 41.1 | 21.4 (monomer) | 23.7 | 24.7 |
| Norrin | 2.74 | 9.18 | 37.4 | 27.2 (dimer) | 33.5 | 22.5 | |
| Norrin–Fz4CRD | deglyc¶ | 3.41 | 11.92 | 93.8 | 61.3 (2:2 complex) | 57.9 | 56.5 |
-
*
Rg is Radius of gyration, calculated from Guinier plot using AutoRg (Petoukhov et al., 2012).
-
†
Dmax is the maximum dimension of the particle, calculated by GNOM (Svergun, 1992).
-
‡
The theoretical molecular weight (MWTheoretical) is predicated from amino acid sequence plus the molecular weight of N-linked glycans (see ‘Materials and methods’, SEC-MELS analysis for detailed information of calculation).
-
§
The measured molecular weight (MWMeasured) is calculated from forward scattering of sample (I(0)) by comparison with reference bovine serum albumin (BSA).
-
#
The measured molecular weight (MWMeasured) is obtained by dividing the Volume Porod (Vp [nm3]) by 1.66 (Rambo and Tainer, 2011).
-
¶
The proteins were produced from HEK293T cells in the presence of kifunensine with limited glycosylation and treated with endoglycosidase-F1.
-
**
The proteins were produced from HEK293T cells with full glycosylation.
Table 3
Molecular properties of the proteins determined by SEC-MALS
| Protein | Number of N-glyc sites | N-Glyc state | MWTheoretical (kDa)‡ | MWMeasured (KDa) |
|---|---|---|---|---|
| Fz4CRD | 2 | deglyc* | 17.1 (monomer) | 15.7 ± 0.4 |
| Fz4CRD | 2 | glyc† | 21.4 (monomer) | 23.6 ± 0.3 |
| mFz5CRD | 2 | glyc† | 22.2 (monomer) | 23.9 ± 0.9 |
| mFz8CRD | 2 | glyc† | 22.1 (monomer) | 23.7 ± 0.2 |
| Norrin–Fz4CRD | 4 (2:2 complex) | deglyc* | 61.3 (2:2 complex) | 60.1 ± 0.4 |
| Norrin–Fz4CRD | 4 (2:2 complex) | glyc† | 69.9 (2:2 complex) | 61.3 ± 0.5 |
-
*
The proteins were produced from HEK293T cells in the presence of the N-glycosylation processing inhibitors, kifunensine resulting in limited glycosylation and were treated with endoglycosidase-F1.
-
†
The proteins were produced from HEK293T cells with full glycosylation.
-
‡
The measured molecular weight (MWMeasured) is in general agreement with theoretical molecular weight (MWTheoretical) predicated based on the primary sequence plus the molecular weight of N-linked glycans (see ‘Materials and methods’, SEC-MELS analysis for detailed information of calculation).
