2024-10-23 REL PDBe PDBe PDBe 2022-09-30 2023-04-05 2023-04-05 2024-10-23 Research Foundation - Flanders (FWO) G0G0619N Belgium Cryo-EM structure for the mouse LEPR-CRH2:Leptin:LEPR-Ig complex following symmetry expansion in combination with local refinement Verstraete K Savvides SN Verschueren KG Tsirigotaki A leptin, LEP-R, obesity, metabolism, energy balance, CYTOKINE Tsirigotaki A Dansercoer A Verschueren KHG Markovic I Pollmann C Hafer M Felix J Birck C Van Putte W Catteeuw D Tavernier J Fernando Bazan J Piehler J Savvides SN Verstraete K Mechanism of receptor assembly via the pleiotropic adipokine Leptin. Nat.Struct.Mol.Biol. US 30 551 563 2023 36959263 doi:10.1038/s41594-023-00941-9 1545-9985 8b7q FULLOVERLAP Mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region Mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region 0 1 2
The mLEP-R ectodomain was C-terminally fused to a trimeric GCN4 isoleucine zipper tag and secreted from HEK93 FreeStyle cells and complexed with refolded mouse leptin produced in E.coli.
Mus musculus 0.444 Leptin Mus musculus 0.018873282999999998
Mouse leptin was produced with an N-terminal His-tag and refolded from inclusion bodies produced in E. coli
1 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHPGGPGSENLYFQGGSTGGVPIQKVQDDTKTLIKTIVTRINDISHTQSVSAKQRVTGLDFIPGLHPILSLS KMDQTLAVYQQVLTSLPSQNVLQIANDLENLRDLLHLLAFSKSCSLPQTSGLQKPESLDGVLEASLYSTEVVALSRLQGS LQDILQQLDVSPEC P41160 Leptin receptor Mus musculus 0.097479391
The mLEP-R ectodomain was C-terminally fused to a trimeric GCN4 isoleucine zipper tag and secreted from HEK93 FreeStyle cells and complexed with refolded mouse leptin produced in E.coli.
2 Homo sapiens LEVO LNLAYPISPWKFKLFCGPPNTTDDSFLSPAGAPNNASALKGASEAIVEAKFNSSGIYVPELSKTVFHCCFGNEQGQNCSA LTDNTEGKTLASVVKASVFRQLGVNWDIECWMKGDLTLFICHMEPLPKNPFKNYDSKVHLLYDLPEVIDDSPLPPLKDSF QTVQCNCSLRGCECHVPVPRAKLNYALLMYLEITSAGVSFQSPLMSLQPMLVVKPDPPLGLHMEVTDDGNLKISWDSQTM APFPLQYQVKYLENSTIVREAAEIVSATSLLVDSVLPGSSYEVQVRSKRLDGSGVWSDWSSPQVFTTQDVVYFPPKILTS VGSNASFHCIYKNENQIISSKQIVWWRNLAEKIPEIQYSIVSDRVSKVTFSNLKATRPRGKFTYDAVYCCNEQACHHRYA ELYVIDVNINISCETDGYLTKMTCRWSPSTIQSLVGSTVQLRYHRRSLYCPDSPSIHPTSEPKNCVLQRDGFYECVFQPI FLLSGYTMWIRINHSLGSLDSPPTCVLPDSVVKPLPPSNVKAEITVNTGLLKVSWEKPVFPENNLQFQIRYGLSGKEIQW KTHEVFDAKSKSASLLVSDLCAVYVVQVRCRRLDGLGYWSNWSSPAYTLVMDVKVPMRGPEFWRKMDGDVTKKERNVTLL WKPLTKNDSLCSVRRYVVKHRTAHNGTWSEDVGNRTNLTFLWTEPAHTVTVLAVNSLGASLVNFNLTFSWPMSKVSAVES LSAYPLSSSCVILSWTLSPDDYSLLYLVIEWKILNEDDGMKWLRIPSNVKKFYIHDNFIPIEKYQFSLYPVFMEGVGKPK IINGFTKDAIDKQQNDAGSTGGSGGSGGSGGSGGSRMKQIEDKIEEILSKIYHIENEIARIKKLIGER P48356 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG singleParticle particle 0.3 7.4 20.0 C8H18N2O4S HEPES 150.0 NaCl sodium chloride
20 mM HEPES, 150 mM NaCl, pH 7.4
 C-flat-1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 99 295 LEICA EM GP
This sample was monodisperse.
 TFS KRIOS FLOOD BEAM OTHER FIELD EMISSION GUN 300 2.7 1.2 2.5 105000.0 GATAN K3 BIOQUANTUM (6k x 4k) 1 13230 45.0 1 141157 7Z3R
Crystal structure for mouse leptin in complex with the IgCRH2-fragment of mLEP-R
 C1 4.02 FSC 0.143 CUT-OFF cryoSPARC version 3.3.2 Symmetry expansion in combination with local refinement
To address the breakage of symmetry in the ring-like core region of the complex and possibly revolve the mLEP-RCRH2:mLeptin:mLEP-RCRH1-IgCRH2 subcomplex at higher resolution, the pseudo-C3 symmetric volume following consenus refinement was aligned to the pseudo-C3 symmetry axis via the Volume Alignment Tool job in cryoSPARC. The associated particle set was re-extracted without binning and symmetry expanded around the C3 axis resulting in 163,914 particles. Using the molmap function in Chimera, a volume blurred to 25 Angstrom around one mLEP-RCRH2:mLeptin:mLEP-RCRH1-IgCRH2 subcomplex was generated, and transformed into a mask with the Volume Tools job in cryoSPARC. Local refinement was performed by limiting the rotation and shift search extent around the original consensus refinement. The center of mass of the mask was used as a fulcrum point. This approach resulted in a cryo-EM map with an FSC0.143 resolution of 4.02 Angstrom in which the crystallographic model for the mLEP-RCRH2:mLeptin:mLEP-R_IgCRH2' complex was fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model.
163914 MAXIMUM LIKELIHOOD cryoSPARC v3.3.1 5 28233.0 cryoSPARC v3.3.1 Ab initio 3D classification emd_15899.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 371.392 371.392 371.392 90.0 90.0 90.0 X Y Z -0.52969044 0.67219245 0.00008679922 0.010363879 0.829 0.829 0.829 0.139 AUTHOR Sharpened cryo-EM map following local refinement following symmetry expansion of particle set FLEXIBLE FIT UCSF Chimera 1.17
The crystallographic model for the mLEP-RCRH2:mLeptin:mLEP-R_IgCRH2' complex (pdb 7z3r) was fitted in the cryo-EM map using Chimera and real-space refined in Phenix using reference restraints to the starting model.
REAL emd_15899_msk_1.map emd_15899_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 371.392 371.392 371.392 90.0 90.0 90.0 X Y Z -0.0018753436 2.0615392 0.00032834534 0.012526691 0.829 0.829 0.829 AUTHOR Sharpened cryo-EM map with DeepEMhancer emd_15899_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 371.392 371.392 371.392 90.0 90.0 90.0 X Y Z -0.20230402 0.51172465 0.00008679921 0.007862856 0.829 0.829 0.829 AUTHOR Non-sharpened map following local refinement following symmetry expansion of particle set emd_15899_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 371.392 371.392 371.392 90.0 90.0 90.0 X Y Z -0.39105016 0.59302545 0.0004297967 0.04408567 0.829 0.829 0.829 AUTHOR Half map A emd_15899_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 371.392 371.392 371.392 90.0 90.0 90.0 X Y Z -0.43750748 0.59916043 0.00042532937 0.04428753 0.829 0.829 0.829 AUTHOR Half map B