Structural basis for Retriever-SNX17 assembly and endosomal sorting
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Eclipse
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Ezra Burstein
PROVIDER: MSV000095676 | MassIVE | Thu Aug 22 14:01:00 BST 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:Supporting raw MS data for paper (doi: 10.1016/j.cell.2024.05.018) by Sinha N.K. et al, titled "The ribotoxic stress response drives UV-mediated cell death".
Index of MS files and labels
Table S1 - HaCaT Timecourse.
1-1 - Proteome (AO3604-3627 | Unimod:35; 2016; 4 | 126 -UT_01; 127n - UT_02; 127c - UT_03; 128n -1min_01; 128c - 1min_02; 129n - 1min_03; 129c - 1min_04; 130n - 5min_01; 130c - 5min_02; 131n - 5min_03; 131c - 15min_01; 132n - 15min_02; 132c - 15min_03; 133n - 30min_01; 133c - 30min_02; 134n - 30min_03)
1-2 - Phospho (AO3628-3651 | Unimod:35; 2016; 4; 21 | 126 -UT_01; 127n - UT_02; 127c - UT_03; 128n -1min_01; 128c - 1min_02; 129n - 1min_03; 129c - 1min_04; 130n - 5min_01; 130c - 5min_02; 131n - 5min_03; 131c - 15min_01; 132n - 15min_02; 132c - 15min_03; 133n - 30min_01; 133c - 30min_02; 134n - 30min_03)
Table S2 - MCF10a KO and inhibitor (Set1 - ZAK & Set 2 - GCN2).
2-1-1 - Proteome (Set 1 - AO4019-4042 | Unimod:35; 2016; 4 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_ZAKi01; 128c - WT_UT_ZAKi02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_ZAKi01; 130c - WT_UV_ZAKi02; 131n - ZAK-KO_UT_DMSO01; 131c - ZAK-KO_UT_DMSO02; 132n - ZAK-KO_UT_ZAKi01; 132c - ZAK-KO_UT_ZAKi02; 133n - ZAK-KO_UV_DMSO01; 133c - ZAK-KO_UV_DMSO02; 134n - ZAK-KO_UV_ZAKi01; 134c -ZAK-KO_UV_ZAKi02)
2-1-2 - Proteome (Set 2 - AO4049-4072 | Unimod:35; 2016; 4 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_GCN2i01; 128c - WT_UT_GCN2i02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_GCN2i01; 130c - WT_UV_GCN2i02; 131n - GCN2-KO_UT_DMSO01; 131c - GCN2-KO_UT_DMSO02; 132n - GCN2-KO_UT_GCN2i01; 132c - GCN2-KO_UT_GCN2i02; 133n - GCN2-KO_UV_DMSO01; 133c - GCN2-KO_UV_DMSO02; 134n - GCN2-KO_UV_GCN2i01; 135n -GCN2-KO_UV_GCN2i02)
2-2-1 - Phospho (Set 1 - AO4013-4019 | Unimod:35; 2016; 4; 21 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_ZAKi01; 128c - WT_UT_ZAKi02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_ZAKi01; 130c - WT_UV_ZAKi02; 131n - ZAK-KO_UT_DMSO01; 131c - ZAK-KO_UT_DMSO02; 132n - ZAK-KO_UT_ZAKi01; 132c - ZAK-KO_UT_ZAKi02; 133n - ZAK-KO_UV_DMSO01; 133c - ZAK-KO_UV_DMSO02; 134n - ZAK-KO_UV_ZAKi01; 134c -ZAK-KO_UV_ZAKi02)
2-2-2 - Phospho (Set 2 - AO4043-4048 | Unimod:35; 2016; 4; 21 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_GCN2i01; 128c - WT_UT_GCN2i02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_GCN2i01; 130c - WT_UV_GCN2i02; 131n - GCN2-KO_UT_DMSO01; 131c - GCN2-KO_UT_DMSO02; 132n - GCN2-KO_UT_GCN2i01; 132c - GCN2-KO_UT_GCN2i02; 133n - GCN2-KO_UV_DMSO01; 133c - GCN2-KO_UV_DMSO02; 134n - GCN2-KO_UV_GCN2i01; 135n -GCN2-KO_UV_GCN2i02)
Table S3 - HaCaT Kinase inhibitors (Set 1 & Set 2).
3-1-1 - Proteome (Set 1 - AO3766-3777 | Unimod:35; 2016; 4 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Nil)_UT01; 129n - ZAKi(Nil)_UT02; 129c - ZAKi(Nil)_UV01; 130n - ZAKi(Nil)_UV02; 130c - p38i_UT01; 131n - p38i_UT02; 131c - p38i_UV01; 132n - p38i_UV02; 132c - JNKi_UT01; 133n - JNKi_UT02; 133c - JNKi_UV01; 134n - JNKi_UV02)
3-1-2 - Proteome (Set 2 - AO3778-3789 | Unimod:35; 2016; 4 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Vem)_UT01; 129n - ZAKi(Vem)_UT02; 129c - ZAKi(Vem)_UV01; 130n - ZAKi(Vem)_UV02; 130c - GCN2i_UT01; 131n - GCN2i_UT02; 131c - GCN2i_UV01; 132n - GCN2i_UV02; 132c - ATRi_UT01; 133n - ATRi_UT02; 133c - ATRi_UV01; 134n - ATRi_UV02)
3-2-1 - Phospho (Set 1 - AO3754-3759 | Unimod:35; 2016; 4; 21 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Nil)_UT01; 129n - ZAKi(Nil)_UT02; 129c - ZAKi(Nil)_UV01; 130n - ZAKi(Nil)_UV02; 130c - p38i_UT01; 131n - p38i_UT02; 131c - p38i_UV01; 132n - p38i_UV02; 132c - JNKi_UT01; 133n - JNKi_UT02; 133c - JNKi_UV01; 134n - JNKi_UV02)
3-2-2 - Phospho (Set 2 - AO3760-3765 | Unimod:35; 2016; 4; 21 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Vem)_UT01; 129n - ZAKi(Vem)_UT02; 129c - ZAKi(Vem)_UV01; 130n - ZAKi(Vem)_UV02; 130c - GCN2i_UT01; 131n - GCN2i_UT02; 131c - GCN2i_UV01; 132n - GCN2i_UV02; 132c - ATRi_UT01; 133n - ATRi_UT02; 133c - ATRi_UV01; 134n - ATRi_UV02).
Tabel S4 - ZAK affinity purification.
4-1 - Label-free ZAK pulldown (mNG-ZAK-WT labeled files | Unimod:35; 4| Untreated or ANS treated cells)
Additional file:
AO4072_GCN2_RSP10_tMS2: Targeted RPS10-Kgg search | Unimod:35; 2016; 4; 492 | TMT label as 2-1-2.
2023-07-25 | MSV000092521 | MassIVE
Project description:The raw data for chemoproteomic experiment of multiple concentrations of IDRB-Probe-2 in Hela. Each concentration includes two measurements taken from distinct samples. 127N and 127C represent the data of 0 μM IDRB-Probe-2. 128N and 128C represent the data of 0.5 μM IDRB-Probe-2. 129N and 129C represent the data of 1.5 μM IDRB-Probe-2. 130N and 130C represent the data of 5 μM IDRB-Probe-2. 131N and 131C represent the data of 15 μM IDRB-Probe-2. 132N and 132C represent the data of 50 μM IDRB-Probe-2. 133N and 133C represent the data of 1000 μM IDRB-Probe-2.
2025-01-06 | PXD058716 | Pride
Project description:Samples 939560 F1-8 are the 8 fractions for the samples A1-D3, as well as F3, G3, H1, and I1 (these 4 were included in both sets and can be used to help normalize between sets). Samples 939560 F1-8 are the 8 fractions for the samples E1-I3, as well as A2 (included in both sets to help with normalization/comparison between sets).
939560:
sample TMT Label
A1 126
A2 127N
A3 127C
B1 128N
B2 128C
B3 129N
C1 129C
C2 130N
C3 130C
D1 131N
D2 131C
D3 132N
F3 132C
G3 133N
H1 133C
I1 134N
939561:
sample TMT Label
E1 126
E2 127N
E3 127C
F1 128N
F2 128C
F3 129N
G1 129C
G2 130N
G3 130C
H1 131N
H2 131C
H3 132N
I1 132C
I2 133N
I3 133C
A2 134N
A1-A3: W minus- MHC> Gal4 (Control)
B1-B3: WT- MHC-Gal4> USP10 OE
C1-C3: WT- MHC-Gal4> USP10 Sh RNAi
D1-D3: WT- MHC-Gal4> USP10 RNAi KK
E1-E3: WT- MHC-Gal4> FMR1 OE
F1-F3: WT- MHC-Gal4> FMR1 RNAi
G1-G3: WT- MHC-Gal4> FMR1 RNAi
H1-H3: WT- MHC-Gal4> RIN OE
I1-I3: WT- MHC-Gal4> RIN RNAi
2025-01-10 | MSV000096824 | MassIVE
Project description:Supporting raw MS data for paper (DOI:10.1083/jcb.202303082) by Paul S. et al., titled "NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis". Index of MS supporting files uploaded: - Related to Figure 6A;S4A (AO3556-AO3579: whole proteome (Unimod: 35; 2016; 4)). - Related to Figure 6A-D;S4B-D (AO3580-AO3603: phospho proteome (Unimod: 35; 21; 2016; 4)). TMTpro channel: WT-UT (126, 127n, 127c, 128n), WT-MRT (128c, 129n, 129c, 130n), TBK1_KO-UT (130c, 131n, 131c, 132n), TBK1_KO-MRT (132c, 133n, 133c, 134n).
2023-11-01 | MSV000093220 | MassIVE
Project description:Proteomic profiling of pils6-1 (mu1047700) and W22 (WIldtype) roots was performed in the presence and absence of auxin treatment (10 uM IAA) for 1 hour. Proteins were extracted and processed using the Phenol-FASP method described in https://doi.org/10.1002/pmic.201800220.
Samples were TMT labeled as follows: WT M_R1+126, WT M_R2+127N, WT M_R3+127C, POOLEDSamples+128N, WT IAA_R1+128C, WT IAA_R2+129N, WT IAA_R3+129C, WT IAA_R4+130N, pils6 M_R1+130C, pils6 M_R2+131N, pils6 M_R3+131C, pils6 M_R4+132N, pils6 IAA_R1+132C, pils6 IAA_R2+133N, pils6 IAA_R3+133C, pils6 IAA_R4+134N.
2023-07-13 | MSV000092438 | MassIVE
Project description:During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms underlying this interaction have remained elusive. Here, we report the structure of the Retriever-SNX17 complex determined using cryogenic electron microscopy (cryo-EM). Our structure reveals that the C-terminal tail of SNX17 engages with a highly conserved interface between the VPS35L and VPS26C subunits of Retriever. Through comprehensive biochemical, cellular, and proteomic analyses, we demonstrate that disrupting this interface impairs the Retriever-SNX17 interaction, subsequently affecting the recycling of SNX17-dependent cargos and altering the composition of the plasma membrane proteome. Intriguingly, we find that the SNX17-binding pocket on Retriever can be utilized by other ligands that share a consensus acidic C-terminal tail motif. By showing how SNX17 is linked to Retriever, our findings uncover a fundamental mechanism underlying endosomal trafficking of critical cargo proteins and reveal a mechanism by which Retriever can engage with other regulatory factors.
| S-EPMC10980035 | biostudies-literature
Project description:Supporting MS data for paper (DOI:10.1016/j.celrep.2024.115179) by Pham, B. et al., titled "mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase". Related to Table S1 - HEK293 - degradomics (HA-2-165 | Unimod:35; 2016; 4 | 126 - Neg Ctrl (WT cells -AHA); 127n - MAEA-WT - UT_0h replicate 1; 127c - MAEA-WT - UT_0h replicate 2; 128n - MAEA-WT - UT_0h replicate 3; 128c - MAEA-WT - UT_10h replicate 1; 129n - MAEA-WT -UT_10h replicate 2; 129c - MAEA-WT - Tor1_10h replicate 1; 130n - MAEA-WT - Tor1_10h replicate 2; 130c - MAEA-WT - Tor1_10h replicate 3; 131n - MAEA[Y394A] - UT_0h replicate 1; 131c - MAEA[Y394A] - UT_0h replicate 2; 132n - MAEA[Y394A] - UT_0h replicate 3; 132c - MAEA[Y394A] - UT_10h replicate 1; 133n - MAEA[Y394A] - UT_10h replicate 2; 133c - MAEA[Y394A] - UT_01h replicate 3; 134n - MAEA[Y394A] - Tor1_10h replicate 1; 134c - MAEA[Y394A] - Tor1_10h replicate 2; 135n - MAEA[Y394A] - Tor1_10h replicate 3)
2024-08-29 | MSV000095724 | MassIVE
Project description:Protein-protein interaction analysis by label-free quantitation.
LUM2_1153149, LUM2_1153150, LUM2_1153151: EV
LUM2_1153152, LUM2_1153153, LUM2_1153154: WT
LUM2_1153155, LUM2_1153156, LUM2_1153157: V205D-R248M
2024-02-16 | MSV000094101 | MassIVE
Project description:Sorting nexins (SNXs) are regulators of endosomal sorting. For the SNX-BAR subgroup, a Bin/Amphiphysin/Rvs (BAR) domain is vital for formation/stabilization of tubular subdomains that mediate cargo recycling. Here, by analysing the in vitro membrane remodelling properties of all 12 human SNX-BARs, we report that some, but not all, can elicit the formation of tubules with diameters that resemble sorting tubules observed in cells. We reveal that SNX-BARs display a restricted pattern of BAR domain-mediated dimerization, and by resolving a 2.8 Å structure of a SNX1-BAR domain homodimer, establish that dimerization is achieved in part through neutralization of charged residues in the hydrophobic BAR-dimerization interface. Membrane remodelling also requires functional amphipathic helices, predicted to be present in all SNX-BARs, and the formation of high order SNX-BAR oligomers through selective 'tip-loop' interactions. Overall, the restricted and selective nature of these interactions provide a molecular explanation for how distinct SNX-BAR-decorated tubules are nucleated from the same endosomal vacuole, as observed in living cells. Our data provide insight into the molecular mechanism that generates and organizes the tubular endosomal network.
| S-EPMC3512392 | biostudies-literature
Project description:During infection chlamydial pathogens form an intracellular membrane-bound replicative niche termed the inclusion, which is enriched with bacterial transmembrane proteins called Incs. Incs bind and manipulate host cell proteins to promote inclusion expansion and provide camouflage against innate immune responses. Sorting nexin (SNX) proteins that normally function in endosomal membrane trafficking are a major class of inclusion-associated host proteins, and are recruited by IncE/CT116. Crystal structures of the SNX5 phox-homology (PX) domain in complex with IncE define the precise molecular basis for these interactions. The binding site is unique to SNX5 and related family members SNX6 and SNX32. Intriguingly the site is also conserved in SNX5 homologues throughout evolution, suggesting that IncE captures SNX5-related proteins by mimicking a native host protein interaction. These findings thus provide the first mechanistic insights both into how chlamydial Incs hijack host proteins, and how SNX5-related PX domains function as scaffolds in protein complex assembly.
| S-EPMC5348129 | biostudies-literature