2025-01-29 REL PDBe PDBe PDBe 2023-09-29 2023-12-27 2023-12-27 2025-01-29 Swiss National Science Foundation TMSGI3_211581 Switzerland Swiss National Science Foundation 310030_185235 Switzerland Swiss National Science Foundation PCEFP3_181282 Switzerland Structure of the mu opioid receptor bound to the antagonist nanobody NbE Yu J Kumar A Zhang X Martin C Raia P Manglik A Ballet S Boland A Stoeber M opioid receptor, nanobody, antagonist, NabFab, MOR, MEMBRANE PROTEIN Yu J Kumar A Zhang X Martin C Van Holsbeeck K Raia P Koehl A Laeremans T Steyaert J Manglik A Ballet S Boland A Stoeber M Structural basis of mu-opioid receptor targeting by a nanobody antagonist. Nat Commun UK 15 8687 8687 2024 39384768 doi:10.1038/s41467-024-52947-6 2041-1723 Yu J Kumar A Zhang X Martin C Raia P Koehl A Laeremans T Steyaert J Manglik A Ballet S Boland A Stoeber M Structural Basis of mu-Opioid Receptor-Targeting by a Nanobody Antagonist. Biorxiv US 2023 38106026 doi:10.1101/2023.12.06.570395 2692-8205 8qot FULLOVERLAP MOR-NbE-NabFab-AntiFab complex MOR-NbE-NabFab-AntiFab complex 0 1 2 3 4 5
Mu-opioid receptor bound to a nanobody antagonist (NbE), and NabFab module used as fiducial marker.
Mus musculus 0.12 Mu-type opioid receptor Mus musculus 0.05399421499999999
MOR-2xSTREP-8xHIS
1 Spodoptera frugiperda LEVO MKTIIALSYIFCLVFADYKDDDDAMGPGNISDCSDPLAPASCSPAPGSWLNLSHVDGNQSDPCGPNRTGLGENLYFQGSH SLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWP FGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGS IDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWT PIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSTILEVLFQGPEQQNSARI RQNTREHPSTANTVDRTNHQLENLEAETAPLPSSLAEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEKGAHHHHHH HH P42866 Nanobody E (NbE) Lama glama 0.018458662
synthesized nanobody NbE-6xHis
1 Escherichia coli LEVO VKKLLFAIPLVVPFYAAQPAMAQVQLVESGGGLVQAGGSLRLSCAASGSISSISTMGWYRQAPGKERELVAAITSGGSTN YADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNFKYYSGSYFYKSEYDYWGKGTPVTVSSAAAHHHHHHGAAEQK LISEEDLNGAA NabFab HC synthetic construct 0.028220525
Signal sequence-NabFab HC
1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSS SSYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDYWGQGTLVTVSSASTKGP SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVN HKPSNTKVDKKVEPKSCDKTHT NabFab LC synthetic construct 0.025794859 1 Escherichia coli LEVO MKKNIAFLLASMFVFSIATNAYASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYS GVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLL NNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC Anti-Fab Nanobody Lama glama 0.017414383000000002
Signal sequence-6xHis Anti-Fab nanobody
1 Escherichia coli LEVO MKYLLPTAAAGLLLLAAQPAMAMHHHHHHGENLYFQGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPG KEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSS singleParticle particle 2.8 7.5 20.0 C8H18N2O4S Hepes 100.0 NaCl Sodium chloride 0.001 C47H88O22 Lauryl maltose neopentyl glycol 0.0001 C31H50O4 Cholesteryl hemisuccinate UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE AIR ETHANE 95 288 LEICA EM GP
MOR receptor was expressed and purified in insect cells in isolation. NbE was expressed and purified in E. coli. NabFab module was expressed and purified in E. coli. All purified components were incubated and formed readily a stable complex. Final complex was purified over size exclusion chromatography.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.6 2.0 150000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 90.0 95.0 FEI FALCON III (4k x 4k) COUNTING 4096 4096 4 5938 52.0 40.0 1 6063911 1 3.2 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 445766 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 RELION 3 emd_18541.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -0.044121403 1.7903484 0.00039334194 0.016585164 0.9759 0.9759 0.9759 0.2 AUTHOR DeepEMhancer sharpened map of the MOR_NbE_NabFab_anti-Fab complex. 4DKL A PDB experimental model 7PHQ A PDB experimental model 7PHQ B PDB experimental model 7PHQ E PDB experimental model AB INITIO MODEL REAL 68.0 emd_18541_msk_1.map emd_18541_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -1.241123 2.9168713 0.00007932839 0.056001887 0.9759 0.9759 0.9759 AUTHOR Unsharpened map of the MOR_NbE_NabFab_anti-Fab complex. emd_18541_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -1.6057428 3.023454 0.00013487152 0.048386544 0.9759 0.9759 0.9759 AUTHOR Unsharpened MOR_NbE map (focused refinement). emd_18541_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -0.097184286 2.1362374 0.00014496614 0.014290846 0.9759 0.9759 0.9759 AUTHOR DeepEMhancer sharpened MOR_NbE map (focused refinement). emd_18541_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -1.9803883 3.2873855 0.00076267356 0.06959388 0.9759 0.9759 0.9759 AUTHOR Half map A of the MOR_NbE map (focused refinement). emd_18541_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -1.9126917 3.59989 0.00077656476 0.06924454 0.9759 0.9759 0.9759 AUTHOR Half map B of the MOR_NbE map (focused refinement). emd_18541_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -1.3490033 3.180665 0.00071277376 0.0684114 0.9759 0.9759 0.9759 AUTHOR Half map A of the MOR_NbE_NabFab_anti-Fab complex. emd_18541_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 312.288 312.288 312.288 90.0 90.0 90.0 X Y Z -1.4301059 3.1045015 0.0006973036 0.06822579 0.9759 0.9759 0.9759 AUTHOR Half map B of the MOR_NbE_NabFab_anti-Fab complex.