Cryo-EM structure of the ternary Netrin 1-Neogenin 1-Repulsive Guidance Molecule B complex

2024-11-06 REL PDBe PDBe PDBe 2021-02-01 2021-03-31 2021-03-31 2024-11-06 Cancer Research UK C20724/A14414 United Kingdom Cancer Research UK C20724/A26752 United Kingdom European Research Council (ERC) 647278 United Kingdom Medical Research Council (MRC, United Kingdom) MR/L017776/1 United Kingdom Medical Research Council (MRC, United Kingdom) MR/L009609/1 United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/15 United Kingdom Wellcome Trust 099675/Z/12/Z United Kingdom Wellcome Trust 090532/Z/09/Z United Kingdom Netherlands Organisation for Scientific Research (NWO) ALW-VICI Netherlands H2020 Marie Curie Actions of the European Commission 289581 Netherlands Cryo-EM structure of the ternary Netrin 1-Neogenin 1-Repulsive Guidance Molecule B complex Robinson RA Griffiths SC Signal transduction, cell surface receptors, neuron regeneration, cell migration, Netrin, Neogenin, Repulsive Guidance Molecule, complex structure, protein-protein interactions, SIGNALING PROTEIN Robinson RA Griffiths SC van de Haar LL Malinauskas T van Battum EY Zelina P Schwab RA Karia D Malinauskaite L Brignani S van den Munkhof MH Dudukcu O De Ruiter AA Van den Heuvel DMA Bishop B Elegheert J Aricescu AR Pasterkamp RJ Siebold C Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling. Cell 184 2103 2021 33740419 doi:10.1016/j.cell.2021.02.045 1097-4172 7ndg FULLOVERLAP Cryo-EM structure of the ternary Netrin 1-Neogenin 1-Repulsive Guidance Molecule B complex Cryo-EM structure of the ternary Netrin 1-Neogenin 1-Repulsive Guidance Molecule B complex 0 1 2 3 Homo sapiens 0.50 Netrin 1 1 1 Mus musculus 0.39 Neogenin 1 2 Homo sapiens 0.039 Repulsive Guidance Molecule B 1 3 Homo sapiens 0.18 Repulsive Guidance Molecule B C-terminal region (chain D) 1 5 Netrin-1 Homo sapiens 0.049227401999999996 3 Homo sapiens LEVO GPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHP PAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKM YNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDD SELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCN LHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCP CKDGVTGITCNRCAKGYQQSRSPIAPCIKGSGTETSQVAPA O95631 Neogenin Mus musculus 0.039268199 3 Homo sapiens LEVO ETGETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKA FNNVGEGIPLYESAVTRPHTVPDPTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKN ANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKI TGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKALGSAGKGSRLPDL GSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH Q7TQG5 Repulsive Guidance Molecule B (C-terminal region) Homo sapiens 0.028104493999999997

Repulsive Guidance Molecule B

3 Homo sapiens LEVO PHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHECTDQKVYQAVTDDLPAAFVDGTT SGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQ VSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIF PSSGTKHHHHHH Q6NW40 RGM domain family member B Homo sapiens 0.013022377

Repulsive Guidance Molecule B

3 Homo sapiens LEVO ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSS TNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGD Q6NW40 CALCIUM ION 4.0078e-05

Repulsive Guidance Molecule B

3 CA 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 12 NAG singleParticle particle 0.07 7.5 10.0 C8H18N2O4S HEPES 150.0 NaCl Sodium chloride 2.0 CaCl2 Calcium chloride 1.0 C12H14Na8O27S8 Sucrose octasulfate, sodium salt 0.01 NaN3 Sodium azide

10 mM HEPES pH 7.5, 150 mM NaCl, 2 mM CaCl2, 1 mM sucrose octasulfate, 0.01% NaN3

PELCO Ultrathin Carbon with Lacey Carbon COPPER CARBON LACEY 3.0 GLOW DISCHARGE 30 OTHER 101.325

Agar Scientific Ultra-thin carbon support film, 3 nm - on lacey carbon. https://www.agarscientific.com/ultra-thin-carbon-support-film-3-nm-on-holey-carbon

ETHANE 95 277.15 FEI VITROBOT MARK IV

Lacey carbon grids with 3 nm ultrathin carbon support film were glow discharged for 30 seconds at high RF level using Harrick Plasma Cleaner, model PDC-002-CE, and then 3.5 microl of the sample was pipetted per grid. Excess protein was blotted away for 3 seconds using filter paper (round filter paper for Vitrobot from Agar Scientific, catalogue number 47000-100) and Vitrobot Mark IV (Thermo Fisher Scientific) (relative force -15) at 95-100% humidity. Grids were plunge frozen in liquid ethane..

The ternary NEO1-NET1-RGMB complex was purified by SEC on a S200 10/300 Increase column with a running buffer of 10 mM HEPES pH 7.5, 150 mM NaCl, 2 mM CaCl2, 1 mM sucrose octasulfate, 0.01% NaN3 at 4 degrees C . The peak fraction containing the ternary complex was diluted to 0.07 mg per ml in SEC buffer.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 -0.5 -0.7000000000000001 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 77.0 VOLTA PHASE PLATE FEI FALCON III (4k x 4k) COUNTING 1 1635 37.26 40.0

Cryo-EM data were collected on a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV with a 50 microm C2 aperture and Volta phase plate (Thermo Fisher Scientific), at the Division of Structural Biology, University of Oxford. Movies were recorded using a FEI Falcon III direct electron detector in electron counting mode using EPU software at a nominal magnification of 96000x, corresponding to a physical pixel size of 0.85 angstrom/pixel. A total dose of 40 electrons per square angstrom was used at a dose rate of 0.77 electrons/pix/sec.

1 280158 1 C3 5.98 FSC 0.143 CUT-OFF RELION 3

In total 1635 movies were collected and drift correction, beam-induced motion and dose-weighting were performed with MotionCor2 RELION 3.1 (Zivanov et al., 2018) for 1635 movies. Contrast transfer function (CTF) was estimated using CTFFIND 4.1 (Rohou and Grigorieff, 2015) implemented in RELION. 280158 particles were picked using Warp (Tegunov and Cramer, 2019). 2D classification in cryoSPARC v2 (Punjani et al., 2017) were performed for these particles and best 2D class averaged with 100674 particles were used to generate ab-initio 3D model with C3 symmetry. C1 symmetry did not generate reasonable 3D model. All Warp picked particles were used for 3D classification in cryoSPARC v2 and the best class with 177056 particles was used for refinement in RELION 3.1 with initial model generated in cryoSPARC v2. Byesian particle polishing improved the resolution to 5.44 angstrom, however the map for RGMB was very weak. Last step of 3D classification without alignment with T regularisation parameter set to 16 was performed and gave one class with more continuous map for RGMB, which was refined to 5.98 angstrom resolution, as estimated using the Fourier shell correlation (FSC) = 0.143 criterion.

68541 MAXIMUM LIKELIHOOD RELION 3 MAXIMUM LIKELIHOOD RELION 3 3 59019.0 RELION 3 emd_12286.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -0.0066733146 0.017858697 0.00019691909 0.0013854764 0.85 0.85 0.85 0.007 AUTHOR ::::EMDATABANK.org::::EMD-12286:::: RIGID BODY FIT

Crystal structure used as a model for fitting and rigid body refinement will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021.

Correlation coefficient emd_12286_msk_1.map emd_12286_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -0.0107479505 0.017858697 0.00007608903 0.0014400748 0.85 0.85 0.85 AUTHOR ::::EMDATABANK.org::::EMD-12286:::: emd_12286_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -0.011915589 0.018034741 0.00007641399 0.001449943 0.85 0.85 0.85 AUTHOR ::::EMDATABANK.org::::EMD-12286:::: emd_12286_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 299.2 299.2 299.2 90.0 90.0 90.0 X Y Z -0.009695268 0.017659688 0.000075764074 0.0014565449 0.85 0.85 0.85 AUTHOR ::::EMDATABANK.org::::EMD-12286::::