Cryo-EM structure of a 2:1 ALK:ALKAL2 complex obtained after re-processing of EMPIAR-10930 data

2025-04-23 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2024-07-17 2025-03-12 2025-03-12 2025-04-23 Research Foundation - Flanders (FWO) G0B4918N Belgium Other government Flanders Institute for Biotechnology (VIB) grant number C0101 Belgium Cryo-EM structure of a 2:1 ALK:ALKAL2 complex obtained after re-processing of EMPIAR-10930 data Felix J De Munck S Bazan JF Savvides SN Complex, receptor tyrosine kinase, CYTOKINE Felix J De Munck S Bazan JF Savvides SN Reanalysis of cryo-EM data reveals ALK-cytokine assemblies with both 2:1 and 2:2 stoichiometries. Plos Biol. US 23 e3003124 e3003124 2025 40208865 doi:10.1371/journal.pbio.3003124 1545-7885 9g5i FULLOVERLAP Cryo-EM structure of a 2:1 ALK:ALKAL2 complex obtained after re-processing of EMPIAR-10930 data Cryo-EM structure of a 2:1 ALK:ALKAL2 complex obtained after re-processing of EMPIAR-10930 data 0 1 2

Sample preparation and data collection was performed by Reshetnyak et al. (Nature, 2021, https://doi.org/10.1038/s41586-021-04140-8). Motion corrected micrographs and an uncleaned particle stack containing 18,053,750 particles were downloaded from EMPIAR entry 10930. All subsequent data processing, refinement en model building was performed by Jan Felix with help from Steven De Munck and Savvas Savvides.

Homo sapiens 0.086 ALK tyrosine kinase receptor Homo sapiens 0.039377559 2 Escherichia coli BL21(DE3) LEVO GTAPKSRNLFERNPNKELKPGENSPRQTPIFDPTVHWLFTTCGASGPHGPTQAQCNNAYQNSNLSVEVGSEGPLKGIQIW KVPATDTYSISGYGAAGGKGGKNTMMRSHGVSVLGIFNLEKDDMLYILVGQQGEDACPSTNQLIQKVCIGENNVIEEEIR VNRSVHEWAGGGGGGGGATYVFKMKDGVPVPLIIAAGGGGRAYGAKTDTFHPERLENNSSVLGLNGNSGAAGGGGGWNDN TSLLWAGKSLQEGATGGHSCPQAMKKWGWETRGGFGGGGGGCSSGGGGGGYIGGNAASNNDPEMDGEDGVSFISPLGILY TPALKVMEGHGEVNIKHYLNCSHCEVDECHMDPESHKVICFCDHGTVLAEDGVSCIVSP Q9UM73 2.7.10.1 ALK and LTK ligand 2 Homo sapiens 0.014640013 1 Escherichia coli BL21(DE3) LEVO GAEPREPADGQALLRLVVELVQELRKHHSAEHKGLQLLGRDYALGRAEAAGLGPSPEQRVEIVPRDLRMKDKFLKHLTGP LYFSPKCSKHFHRLYHNTRDCTIPAYYKRCARLLTRLAVSPVCMEDKQ Q6UX46 singleParticle particle 1 7.4 15.0 HEPES 150.0 NaCl 3.0 PEG4000 Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE ETHANE 95 283.15 FEI VITROBOT MARK IV

QUANTIFOIL R1.2/1/3 gold 300 mesh grids without glow-discharge, blotting time 3 sec., blotting force -5..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.5 1.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 96.0 98.0 GIF Bioquantum 20

SerialEM coma-free alignment

GATAN K3 (6k x 4k) 1 13618 4.2 81.0 1 18053705

cryoSPARC Ab-Initio Reconstruction.

C1 3.2 FSC 0.143 CUT-OFF RELION 5

Final 3D refinement was performed in Relion v5 with enabled Blush Regularization.

142986 OTHER cryoSPARC 4.5

Stochastic gradient descent (SGD).

MAXIMUM LIKELIHOOD cryoSPARC 4.5 3 cryoSPARC 4.5 emd_51087.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.456 211.456 211.456 90.0 90.0 90.0 X Y Z -0.057428874 0.10045845 0.000117186944 0.0022986536 0.826 0.826 0.826 0.02 AUTHOR ::::EMDATABANK.org::::EMD-51087:::: Regularly sharpened map of the 2:1 ALK-ALKAL2 complex, obtained after re-processing of EMPIAR-10930 data. 7N00 PDB experimental model OTHER

Rigid-body fitting in Chimera was followed by manual building in Coot and refinement using Phenix real-space refine and Refmac-Servalcat.

REAL emd_51087_msk_1.map emd_51087_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.456 211.456 211.456 90.0 90.0 90.0 X Y Z -0.0016959488 1.6879209 0.0012118649 0.026043126 0.826 0.826 0.826 AUTHOR ::::EMDATABANK.org::::EMD-51087:::: DeepEMhancer sharpened map of the 2:1 ALK-ALKAL2 complex, obtained after re-processing of EMPIAR-10930 data. emd_51087_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.456 211.456 211.456 90.0 90.0 90.0 X Y Z -0.019453814 0.053061064 -0.000029518369 0.001721335 0.826 0.826 0.826 AUTHOR ::::EMDATABANK.org::::EMD-51087:::: Half map 2 of the 2:1 ALK-ALKAL2 complex, obtained after re-processing of EMPIAR-10930 data. emd_51087_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.456 211.456 211.456 90.0 90.0 90.0 X Y Z -0.018376978 0.058741577 -0.000029690988 0.0017192926 0.826 0.826 0.826 AUTHOR ::::EMDATABANK.org::::EMD-51087:::: Half map 1 of the 2:1 ALK-ALKAL2 complex, obtained after re-processing of EMPIAR-10930 data.