Reagents and tools table
| Reagent/resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Antibodies | ||
| Rabbit anti-V5 | Cell Signaling Technology | Cat# 13202; RRID:AB_2687461 |
| Rabbit anti-UHRF1BP1 (BLTP3A) | Bethyl Laboratories | Cat# A304-646A; RRID:AB_2620841 |
| Mouse anti-alpha tubulin | Sigma-Aldrich | Cat# T6793, RRID:AB_477585 |
| Mouse anti-VAMP7 | Synaptic Systems | Cat# 232 011, RRID:AB_2619947 |
| Mouse anti-VAMP4 | Proteintech | Cat# 67219-1-Ig, RRID:AB_2882510 |
| Rabbit anti-ATG9A | Abcam | Cat# ab108338, RRID:AB_10863880 |
| Mouse anti-GAPDH | Thermo Fisher Scientific | Cat# MA5-15738, RRID:AB_10977387 |
| Mouse anti-vinculin | Millipore-Sigma | Cat# SAB4200729, RRID:AB_2877646 |
| Mouse anti-LAMP1 | DSHB | Cat# H4A3, RRID:AB_2296838 |
| Rat anti-Galectin 3 | BioLegend | Cat# 125402, RRID:AB_1134238 |
| Mouse anti-Rab7 | Cell Signaling Technology | Cat# 95746S, RRID:AB_2800252 |
| Rabbit anti-pRab7 | Abcam | Cat# ab302494, RRID:AB_2933985 |
| Recombinant DNA | ||
| pmCh-N1 BLTP3A | De Camilli lab | RRID:Addgene_241246 |
| pEGFP-N1 BLTP3A | De Camilli lab | RRID:Addgene_241247 |
| pmCh-N1 BLTP3B | De Camilli lab | RRID:Addgene_241248 |
| pmCh-N1 BLTP3A LIR mutant | De Camilli lab; this manuscript | RRID:Addgene_241249 |
| pmCh-N1 BLTP3A 1-336 | De Camilli lab; this manuscript | RRID:Addgene_241250 |
| pmCh-N1 BLTP3 chimera-1 | De Camilli lab; this manuscript | RRID:Addgene_241251 |
| pmCh-N1 BLTP3 chimera-2 | De Camilli lab; this manuscript | RRID:Addgene_241252 |
| pmCh-N1 BLTP3A 1-1327 | De Camilli lab; this manuscript | RRID:Addgene_241253 |
| pmCh-N1 BLTP3A 1-1364 | De Camilli lab; this manuscript | RRID:Addgene_241254 |
| pmCh-C1 Rab45 | De Camilli lab | RRID:Addgene_241255 |
| PX458 BLTP3A knockout | De Camilli lab; this manuscript | RRID:Addgene_241256 |
| mScarlet-LRRK1 D1409A | De Camilli lab; credit to Xinbo Wang | RRID:Addgene_241257 |
| pEGFP-N1 LAMP1 | Addgene | RRID:Addgene_34831 |
| GFP-LRRK1 K746G | MRC Reagents and Services | DU67083 |
| RFP-LRRK1 K746G | De Camilli lab | RRID:Addgene_233586 |
| GFP-Rab7 wt | Addgene | RRID:Addgene_61803 |
| GFP-Rab7 Q67L | Addgene | RRID:Addgene_169038 |
| GFP-Rab7 T22N | Addgene | RRID:Addgene_28048 |
| pmApple IST1 | Kind gift from Phyllis Hanson, University of Michigan School of Medicine, Ann Arbor, MI | An RRID does not exist for this resource. |
| NPC1-GFP | Addgene | RRID:Addgene_53521 |
| GFP-LC3B | Addgene | RRID:Addgene_11546 |
| mito-BFP | Addgene | RRID:Addgene_49151 |
| Experimental models | ||
| hTERT-RPE1 | ATCC | CRL-4000; RRID:CVCL_4388 |
| A549 wild-type | ATCC | CCL-185; RRID:CVCL_0023 |
| A549 BLTP3A^V5, B6 clone | De Camilli lab | RRID:CVCL_E9W3 |
| A549 BLTP3A^V5, C5 clone | De Camilli lab | RRID:CVCL_E9W4 |
| A549 BLTP3A knockout, Clone D9 | De Camilli lab | RRID:CVCL_E9W2 |
| A549 BLTP3A knockout, Clone C2 | De Camilli lab | RRID:CVCL_E9W1 |
| A549 VPS13C knockout | De Camilli lab | RRID: CVCL_E6IP |
| C57BL/6J mice | Jackson Laboratory | RRID:IMSR_JAX:000664 |
| Software | ||
| ImageJ | Fiji | RRID:SCR_002285 |
| GraphPad Prism | GraphPad Prism (RRID:SCR_002798) | RRID:SCR_002798 |
| AlphaFold | AlphaFold (RRID:SCR_025454) | RRID:SCR_025885 |
| ConSurf Database | ConSurf Database (RRID:SCR_002320) | RRID:SCR_002320 |
| Velox | Thermo FIsher Scientific | An RRID does not exist for this resource. |
| SIFT based MATLAB script | Github/Zenodo | 10.5281/zenodo.15677643 |
| ImageJ code: Analysis script_0 | Github/Zenodo | 10.5281/zenodo.15653077 |
| Python code: Figure generating script | Github/Zenodo | 10.5281/zenodo.15652924 |
| Chemicals, enzymes and other reagents | ||
| FuGene HD | Promega | Cat# E2311 |
| Lipofectamine 2000 | Invitrogen | Cat# 11668019 |
| PolyJet™ | SignaGen Laboratories | Cat# SL100688 |
| Opti-Mem | Thermo Fisher Scientific | Cat# 31985062 |
| SDS | American Bio | Cat# AB01920-00500 |
| Tris | American Bio | Cat# AB02000-05000 |
| NaCl | Sigma-Aldrich | Cat# 3624-05 |
| Tween-20 | Sigma-Aldrich | Cat# P7949 |
| Bromphenol Blue | Sigma-Aldrich | Cat# B5525 |
| B-mercaptoethanol | Sigma-Aldrich | Cat# M3148 |
| Glycerol | American Bio | Cat# AB00751 |
| Methanol | Sigma-Aldrich | Cat# 179337-4L-PB |
| COmplete mini EDTA Free | Roche | Cat# 11836170001 |
| Precision Plus Protein Dual Color Standards | Biorad | Cat# 1610374 |
| 4–15% MiniPROTEAN 10-well | Biorad | Cat# 4568084 g |
| 4–15% MiniPROTEAN 15-well | Biorad | Cat# 4568086 |
| Nitrocellulose Membrane, Precut, 0.2 µm, 7 ×8.4 cm | Biorad | Cat# 1620146 |
| 10x Tris/Glycine Buffer | Biorad | Cat# 1610771 |
| 10x Tris/Glycine/SDS Buffer | Biorad | Cat# 1610772 |
| Nonfat Dry Powder Milk | Research Products International | Cat# M17200-500.0 |
| Odyssey Classic Imager | LICORbio | RRID:SCR_023765 |
| Dragonfly 200 Confocal Microscope | Andor | An RRID does not exist for this resource. |
| BSA | Sigma-Aldrich | Cat# A9647 |
| Saponin | Sigma-Aldrich | Cat# 84510, CAS: 8047-15-2 |
| Paraformaldehyde 16% Aqueous Solution EM Grade | Electron Microscopy Sciences | Cat# 15710 |
| ProLong™ Gold Antifade Mountant with DNA Stain DAPI | Thermo Fisher Scientific | Cat# P36935 |
| Fisherbrand™ Superfrost™ Disposable Microscope Slides | Thermo Fisher Scientific | Cat# 12-550-143 |
| Circular Cover Glass, 18 mm, #1½, 1 oz | Electron Microscopy Sciences | Cat# 72222-01 |
| Ampicillin sodium salt | Sigma-Aldrich | Cat# A0166, CAS: 69-52-3 |
| Kanamycin | Sigma-Aldrich | Cat# K1377, CAS: 25389-94-0 |
| LB Broth | BD | Cat# 244610 |
| HIFI DNA Assembly Master Mix | NEB | Cat# E2621L |
| NEB® 5-alpha Competent E. coli (High Efficiency) | NEB | Cat# C2987H |
| One Shot™ TOP10 Chemically Competent E. coli | Thermo Fisher Scientific | Cat# C404003 |
| Ethanol | Decon Laboratories | Cat# 2716 |
| GoTaq® DNA Polymerase | Promega | Cat# M3001 |
| Phusion™ Hot Start II DNA Polymerase | Thermo Fisher Scientific | Cat# F549L |
| Bacteriological Petri Dishes | Fisher | Cat# 08757100D |
| Leu-Leu methyl ester hydrobromide (LLOMe) | Sigma-Aldrich | Cat# L7393-500MG, CAS: 1668914-8 |
| GPN | Santa Cruz Biotechnology | Cat# sc-252858; CAS: 14634 |
| Monosodium Urate Crystals | AdipoGen | Cat# AGCR139502002 |
| Alt-R™ CRISPR-Cas9 tracrRNA, ATTO™ 550, 5 nmol | Integrated DNA Technologies | Cat# 1075934 |
| Alt-R™ S.p. HiFi Cas9 Nuclease V3, 100 µg | Integrated DNA Technologies | Cat# 1081060 |
| Alt-R™ HDR Enhancer V2, 30 µL | Integrated DNA Technologies | Cat# 10007910 |
| Geneticin™ Selective Antibiotic (G418 Sulfate) (50 mg/mL) | Thermo Fisher Scientific | Cat# 10131027 |
| V5-Trap® Magnetic Agarose | ChromoTek | Cat# v5tma-20 |
| Triton X-100 | American Bioanalytical | Cat# ab02025 |
| Protease inhibitor tablets | Sigma-Aldrich | Cat# 11836170001 |
| FEI Talos L120C TEM and STEM | Thermo Fisher Scientific | RRID:SCR_019908 |
| Zeiss Versa XRM-620 | Zeiss | An RRID does not exist for this resource. |
| Leica EM ACE600 High Vacuum Sputter Coater | Leica Microsystems | RRID:SCR_020237 |
| 35 mm Dish No. 1.5 Gridded Coverslip 14 mm Glass Diameter | MatTek | Cat# P35G-1.5-14-CGRD |
| Aqueous Glutaraldehyde EM Grade 25% | Electron Microscopy Sciences | Cat# 16220 |
| Sodium Cacodylate Buffer, 0.2 M, pH 7.4 | Electron Microscopy Sciences | Cat# 11652 |
| Osmium Tetroxide 4% Aqueous Solution | Electron Microscopy Sciences | Cat# 19140 |
| Potassium hexacyanoferrate(II) trihydrate, K4Fe(CN)6 | Sigma-Aldrich | Cat# P3289, CAS: 14459-95-1 |
| Uranyl Acetate | Electron Microscopy Sciences | Cat# 22400, CAS: 541-09-3 |
| EMbed 812 Resin | Electron Microscopy Sciences | Cat# 14900 |
| UranyLess EM Stain | Electron Microscopy Sciences | Cat# 22409 |
| Lead Citrate 3% | Electron Microscopy Sciences | Cat# 22410 |
| Durcupan™ Acm Epoxy Resin | Electron Microscopy Sciences | Cat# 14040 |
| DL-dithiothreitol (DTT) | AmericanBio | Cat# AB00490-00010 |
| Ammonium bicarbonate (ABC) | Thermo Scientific | Cat# 393212500 |
| Urea | Thermo Scientific | Cat# 434720050 |
| 2-iodoacetamide (IAA) | Sigma-Aldrich | Cat# I6125-5G |
| trifluoroacetic acid (TFA) | Thermo Scientific | Cat# 85183 |
| acetonitrile (ACN) | Sigma-Aldrich | Cat# 900667-100 ML |
| Formic acid (FA) | Thermo Fisher Scientific | Cat# 28905 |
| HPLC-grade water | Thermo Fisher Scientific | Cat# 268300010 |
| Trypsin Protease | Thermo Fisher Scientific | Cat# 90058 |
| HEPES | Sigma-Aldrich | Cat# H4034-100G |
| Live Cell Imaging Solution | Invitrogen | Cat# A59688DJ |