Structure of the P1B7 antibody bound to the Sotorasib-modified KRas G12C peptide presented by the A*03:01 MHC I complex

2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.title _citation.year _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2023-09-28 2024-10-16 2024-10-16 2025-05-14 National Institutes of Health/National Cancer Institute (NIH/NCI) P41-GM103393 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) T32 GM 064337 United States Howard Hughes Medical Institute (HHMI) United States Structure of the P1B7 antibody bound to the Sotorasib-modified KRas G12C peptide presented by the A*03:01 MHC I complex Chan LM Roweder PJ Craik CS Verba KA antibody, MHC, haptenated peptide, PEPTIDE BINDING PROTEIN, IMMUNE SYSTEM Pandey A Rohweder PJ Chan LM Ongpipattanakul C Chung DH Paolella B Quimby FM Nguyen N Verba KA Evans MJ Craik CS Therapeutic Targeting and Structural Characterization of a Sotorasib-Modified KRAS G12C-MHC I Complex Demonstrate the Antitumor Efficacy of Hapten-Based Strategies. Cancer Res. US 85 329 341 2025 39656104 doi:10.1158/0008-5472.CAN-24-2450 1538-7445 0400 CNREA8 8udr FULLOVERLAP P1B7 antibody:V7-Sotorasib A*03:01 MHC I complex P1B7 antibody:V7-Sotorasib A*03:01 MHC I complex 0 1 2 4 5 3 Homo sapiens 0.127044 HLA class I histocompatibility antigen, A alpha chain Homo sapiens 0.031757953 1 Escherichia coli LEVO GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGT LRGYYNQSEAGSHTIQIMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHEAEQLRAYL DGTCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE P04439 Beta-2-microglobulin Homo sapiens 0.011748159999999999 1 Escherichia coli LEVO IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYAC RVNHVTLSQPKIVKWDRDM P61769 GTPase KRas, N-terminally processed Homo sapiens 0.000889094 1 LEVO VVVGACGVGK P01116 P1B7 Heavy Chain Homo sapiens 0.024103028999999998 1 Homo sapiens LEVO VQLQQSGPGLVKPSQTLSLTCAISGDSVSSNSVAWNWIRQSPSRGLEWLGRTYYRSKWYSDYAVSVKSRITINPDTSKNQ FSLQLTSMTPEDTAVYYCAREGVTMGPGAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC P1B7 Light Chain Homo sapiens 0.022580805 1 Homo sapiens LEVO ALTQPPSVSGSPGQSVTISCTGSSSDVGHYNRVSWYQQSPGTAPKLMIYDVSNRPSGAFSRFSGSRSGNTASLTISGLQP EDEADYYCSSHRTGYTVEVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKA GVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE AMG 510 (bound form) 0.00056261 1 MOV singleParticle particle 0.0762 7.5 20.0 C8H18N2O4S HEPES 100.0 KCl Potassium Chloride

20mM HEPES ph 7.5, 100 mM KCl

Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GRAPHENE OXIDE ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 7.0 20.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 10 GATAN K3 (6k x 4k) 1 3795 2.0 45.8 1 1375850 cryoSPARC 3.2.0 Patch CTF PHASE FLIPPING AND AMPLITUDE CORRECTION 3.1 FSC 0.143 CUT-OFF cryoSPARC 3.2.0 NU-Refinement 286405 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_42151.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 293.91998 293.91998 293.91998 90.0 90.0 90.0 X Y Z -3.0880804 4.8604445 -0.000117179006 0.06260596 0.835 0.835 0.835 0.404 AUTHOR ::::EMDATABANK.org::::EMD-42151:::: emd_42151_msk_1.map emd_42151_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 293.91998 293.91998 293.91998 90.0 90.0 90.0 X Y Z -0.40584153 1.0992525 -0.00011717901 0.021451177 0.835 0.835 0.835 AUTHOR ::::EMDATABANK.org::::EMD-42151:::: emd_42151_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 293.91998 293.91998 293.91998 90.0 90.0 90.0 X Y Z -0.48792496 1.1496627 0.00027114764 0.027086843 0.835 0.835 0.835 AUTHOR ::::EMDATABANK.org::::EMD-42151:::: emd_42151_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 293.91998 293.91998 293.91998 90.0 90.0 90.0 X Y Z -0.43750322 1.1679356 0.0002675209 0.027160792 0.835 0.835 0.835 AUTHOR ::::EMDATABANK.org::::EMD-42151::::