2025-07-02 REL PDBj 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 STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature refine _em_admin.last_update _pdbx_entry_details.has_protein_modification _refine.ls_d_res_high _refine.ls_d_res_low DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBj PDBj 2023-01-15 2023-03-29 2023-03-29 2025-07-02 Japan Society for the Promotion of Science (JSPS) Japan Cryo-EM structure of the zeaxanthin-bound kin4B8 Murakoshi S Chazan A Shihoya W Beja O Nureki O Rhodopsin, Cryo-EM, anntena, PROTON TRANSPORT Chazan A Das I Fujiwara T Murakoshi S Rozenberg A Molina-Marquez A Sano FK Tanaka T Gomez-Villegas P Larom S Pushkarev A Malakar P Hasegawa M Tsukamoto Y Ishizuka T Konno M Nagata T Mizuno Y Katayama K Abe-Yoshizumi R Ruhman S Inoue K Kandori H Leon R Shihoya W Yoshizawa S Sheves M Nureki O Beja O Phototrophy by antenna-containing rhodopsin pumps in aquatic environments. Nature UK 615 535 540 2023 36859551 doi:10.1038/s41586-023-05774-6 1476-4687 0006 NATUAS 8i2z FULLOVERLAP Kin4B8 Kin4B8 0 1 uncultured Bdellovibrionales bacterium Xanthorhodopsin uncultured Bdellovibrionales bacterium 0.028745842 1 Escherichia coli LEVO MSATTLTLQQFSTVYNMLSFAVASMLGAFAFFVMGRKIVGPKYRLALVVSSLVVLIAGYHYWRIMGSWTAAYALKDGMYV PTGEPFNDAYRYVDWLLTVPLLLTELVLVMKLKKESGSVLAKLILAAIAMIALGYPGEISNPESQAGARLMWGVLSTVPF LYILYVLWVRLGDAIGEHPAKVQVLLKNTRYLILLTWGFYPIVYAMGSYGWLGGAGSVVAVQVGYSIADVTAKALYGVMI FAIAYAKSEADGSLPAHHHHHH A0A977XLG0 RETINAL 0.00028443599999999994 1 RET Zeaxanthin 0.000568871 1 K3I water 1.8015e-05 33 HOH singleParticle particle 8.0 150.0 NaCl sodium chloride 20.0 C4H11NO3 tris hydroxymethyl aminomethane
150 mM NaCl, 20 mM Tris-HCl
 Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE OTHER ETHANE 100 277
Vitrification carried out in ethane atmosphere..
TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 1.6 GATAN K3 (6k x 4k) 50.14 1 RELION 3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.3 FSC 0.143 CUT-OFF 4337540 MAXIMUM LIKELIHOOD cryoSPARC 2.0 MAXIMUM LIKELIHOOD cryoSPARC 2.0 emd_35143.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 130 134 108 113 114 122 130 134 108 107.9 111.22 89.64 90.0 90.0 90.0 X Y Z -7.4783454 11.259563999999999 0.000655529 0.93943554 0.83 0.83 0.83 2.0 AUTHOR emd_35143_msk_1.map emd_35143_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 206 206 140 77 77 110 206 206 140 170.98 170.98 116.2 90.0 90.0 90.0 X Y Z -0.30503917 1.1230985 0.013549027 0.09853251 0.83 0.83 0.83 AUTHOR emd_35143_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 206 206 140 77 77 110 206 206 140 170.98 170.98 116.2 90.0 90.0 90.0 X Y Z -0.34291327 1.1106546 0.013452894 0.09871526 0.83 0.83 0.83 AUTHOR