Article
column (GE Healthcare). The column was washed with 1 column volume
(CV) of a linear gradient from 0 to 10% buffer B (20 mM BTP pH 8.6, 1 M
NaCl, 0.004% LMNG), 6 CV at 10% B, 1 CV from 10 to 40% B then 6 CV at
40% B before being re-equilibrated into buffer A. In some cases, a longer
linear gradient was used instead of a stepped elution. This involved 1
CV from 0% B to 5% B, 5 CV 5% B then 20 CV from 5 to 40% B. Protein
elution was monitored by tracking tryptophan fluorescence at λex of
280 nm and λem of 340 nm. Upon completion, the reaction was sup-
plemented with CaCl 2 to a final concentration of 2 mM and applied to
an equilibrated M1–Flag immunoaffinity resin and washed with buffer
containing 0.004% LMNG, 0.004% CHS, 20 mM HEPES pH 7.4, 100 mM
NaCl, 0.2 μM NTS8–13, 2 mM CaCl 2. The receptor was eluted with buffer
containing 100 mM NaCl, 20 mM HEPES pH 7.4, 0.004% LMNG, 0.004%
CHS, 0.2 μM NTS8–13, 0.2 mg ml−1 1× Flag peptide (DYKDDDDK), 5 mM
EDTA. Elution fractions containing receptor were pooled and used for
arrestin complexing.
Analytical fluorescence size-exclusion chromatography for
construct screening
In a final volume of 20 μl, NTSR1 (4.5 μM), the respective arrestin con-
struct (9 μM) and NTS8–13 peptide (50 μM) were incubated in buffer
containing 20 mM HEPES pH 7.4, 100 mM NaCl, 0.004% LMNG, 0.0004%
CHS and 0.2 μM NTS8–13. Using a Prominence-i LC autosampler (Shi-
madzu), 10 μl was injected onto a ENrich size-exclusion chromatogra-
phy 650 10 × 300 column (Bio-Rad) pre-equilibrated in 20 mM HEPES
pH 7.4 100 mM NaCl, 0.004% LMNG, 0.004% CHS and 0.2 μM NTS8–13,
and run at a flow rate of 0.8 ml min−1. Tryptophan fluorescence was
monitored at λex of 280 nm and λem of 340 nm.
Formation and purification of NTSR1–βarr1(ΔCT) complex
For cryo-EM, phosphorylated NTSR1 was mixed in an equimolar ratio
with βarr1(ΔCT) and diC8-PtdIns(4,5)P 2 at a concentration of around
5 μM and supplemented with NTS8–13 to 10 μM final concentration.
The mixture was incubated at 25 °C for 30 min before being concen-
trated with a 50 kDa molecular weight cut-off concentrator (Amicon
or Vivaspin) to around 350 μl and purified by size-exclusion chroma-
tography using two Superdex 200 Increase 10/300 GL columns (GE
Healthcare) connected in tandem. The mobile phase used was 20 mM
HEPES pH 7.4, 100 mM NaCl, 0.00075% LMNG, 0.00025% GDN 0.0001%
CHS and 0.2 μM NTS8–13. Fractions containing complex were combined
and diluted to 1 μM final concentration, and sulfo-LC-SDA (also known
as sulfo-NHS-LC-diazirine; sulfosuccinimidyl 6-(4,4′-azipentanamido)
hexanoate) (Thermo Fisher) as a solution in DMSO was added to 250 μM
final concentration, and such that the final DMSO concentration was
below 4%. The reaction was allowed to proceed for 45 min at 25 °C in
the dark, before hydroxylamine was added to a final concentration of 3
mM and incubated for an additional 15 min. The sample was distributed
into a clear 96-well plate (90 μl per well), put on ice and irradiated for
45 min using a UVL-56 lamp. The sample was then pooled and concen-
trated to around 500 μl then re-run on size-exclusion chromatogra-
phy, again using two Superdex 200 Increase 10/300 GL columns (GE
Healthcare) connected in tandem. Peak fractions were combined and
concentrated with a 100 kDa molecular weight cut-off concentrator
(Amicon) to a final concentration of 4.5 mg ml−1.
Cryo-EM sample preparation and image acquisition
An aliquot of 3.5 μl NTSR1–βarr1(ΔCT) sample was deposited onto glow-
discharged 200 mesh grids (Quantifoil R1.2/1.3) and plunge-frozen into
liquid ethane using an FEI Vitrobot Mark IV (Thermo Fisher Scientific).
Several sessions of data collection were conducted on the same Titan
Krios equipped with an energy filter and operated at 300 keV using a
nominal magnification of 130,000×. Movies were captured using a
Gatan K2 Summit direct electron detector in counted mode, which
resulted in a pixel size of 1.06 Å. Movie stacks were obtained with a
defocus range of −1.0 to −2.0 μm, using SerialEM 3.7.10^48 with a set of
customized scripts enabling automated low-dose image acquisition.
Each movie stack was recorded for a total of 8 s with 0.2 s per frame. The
exposure rate was seven electrons per pixel per second. Initial datasets
were collected by one exposure per hole per single stage movement
but subsequent collections used nine-hole exposures per single stage
movement with beam-tilt compensated by using multi-record strategy
implemented in SerialEM 3.7.10.Cryo-EM data processing
A total of 18,797 image stacks were subjected to beam-induced motion
correction using MotionCor2^49. Contrast transfer function parameters
for each micrograph were estimated from the exposure-weighted aver-
ages of all frames by Gctf v.1.06^50. The following processes were all per-
formed using RELION 3.0^51 , except those mentioned specifically. After
2D classification, 2,628,700 particles were divided into 6 subsets for
3D classification. A reference map for 3D classification was generated
by the ‘3D initial model’ script in RELION 3.0 using default stochastic
gradient descent parameters. All stable classes were then combined for
3D refinement, which led to a 4.5 Å map. Further 3D classification of this
particle set resulted in two best classes with a total of 263,965 particles.
The resulting Bayesian polished particles were used to build the final
map with an overall resolution of 4.2 Å, as determined by Fourier shell
correlation (FSC) using a cutoff of 0.143. To probe the conformational
dynamics, multi-body refinement was performed on the 4.2 Å map
with two bodies corresponding to NTSR1 and βarr1. Local resolution
was estimated with the Bsoft 2.0.6 package^52 (Extended Data Fig. 6b).Model building and refinement
The initial template for NTSR1–βarr1(ΔCT) was built from the receptor
coordinates of the crystal structure of NTSR1–NTS8–13 (RCSB Protein
Data Bank (PDB): 4GRV) and arrestin coordinates from the V2Rpp–βarr1
structure (PDB: 4JQI). The initial coordinates for the NTS8–13 ligand
were taken from the NTSR1–NTS8–13 crystal structure (PDB: 4GRV).
Models were docked into the electron microscopy density map using
UCSF Chimera 1.14^53 , then refined by several iterations of automated
refinement in PHENIX interspersed with manual adjustments in Coot
0.8.9^54. The NTSR1 C terminus was built on the basis of the structure
of V2Rpp bound to βarr1 (PDB: 4JQI). The final model was subjected
to global refinement and minimization in real space using phenix.real_
space_refine in PHENIX v.1.16^55. MolProbity 4.5 was used to evaluate
model geometry^56 (Extended Data Table 1). FSC curves were calculated
between the resulting model and the half map used for refinement as
well as between the resulting model and the other half map for cross-
validation (Extended Data Fig. 6a).Phosphoproteomics experiments
Receptor samples were denatured, reduced, alkylated and digested
according to the manufacturers’ protocols (Protifi). In brief, 5–10 μg
of receptor sample in 0.004% LMNG/0.0004% CHS buffer was diluted
twofold with buffer containing approximately 10% SDS and 100 mM
triethylammonium bicarbonate (TEAB, Sigma) pH 7.6. Cysteine resi-
dues were reduced by the addition of freshly dissolved dithiothreitol
(Sigma) to 20 mM final concentration and heated to 95 °C for 10 min.
Samples were cooled to room temperature and iodoacetamide (Sigma)
was added to 40 mM final concentration. Samples were incubated
for 30 min with light excluded at 25 °C with gentle agitation using a
Thermomixer. Phosphoric acid (12%) was added to lower the pH for
binding to the S-trap column, followed by binding buffer: 90% metha-
nol, 100 mM TEAB pH 7.1. The sample was then added to the S-trap and
sequentially spun at 4,000g until all material was loaded discarding
the flow-through. The column was washed three times with binding
buffer, as above. Freshly reconstituted Trypsin/LysC (Promega) was
diluted into 50 mM TEAB pH 8 supplemented with 0.02% protease
max (Promega) and added to the S-trap (Protifi). The column was
placed inside a clean microcentrifuge tube and incubated at 47 °C in a