Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2

2026-07-08 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.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2024-01-17 2025-01-29 2025-01-29 2026-07-08 EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND 847543 Germany Cryo-EM structure of the light-driven sodium-pumping rhodopsin KR2 Kovalev K Linares R retinal, ion transport, sodium, rhodopsin, photocycle, pentamer, MEMBRANE PROTEIN Gemin O Armijo V Lecomte L Hons M Deckers T Bissardon C Rossi C Lauzier K Janocha R Felisaz F Sinoir J Linares R Babenko A Kovalev K Prokhorova I Khusainov I Schreiner C Kolesnikova O Salo VT Schneider S Bowler MW Wolff G Galej WP Mahamid J Muller CW Carugo KD Eustermann S Mattei S Cipriani F Papp G EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control. Nat.Methods US 2026 42337080 doi:10.1038/s41592-026-03127-5 1548-7105 8rq5 FULLOVERLAP EMDB EMD-19434 associated EM volume

Sodium-pumping rhodopsin Sodium-pumping rhodopsin 0 1

KR2 rhodopsin solubilized in DDM

Dokdonia eikasta 0.15 Sodium pumping rhodopsin Dokdonia eikasta 0.031540438999999997 5 Escherichia coli LEVO MTQELGNANFENFIGATEGFSEIAYQFTSHILTLGYAVMLAGLLYFILTIKNVDKKFQMSNILSAVVMVSAFLLLYAQAQ NWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVVSLTTSKFSSVRNQFWFSGAMMIITGYIGQFYE VSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKILSNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGV MARQLVYTIADVSSKVIYGVLLGNLAITLSKNKELVEANS N0DKS8 (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 0.00035654 5 OLC EICOSANE 0.000282547 66 LFA RETINAL 0.00028443599999999994 5 RET SODIUM ION 2.299e-05 5 NA OLEIC ACID 0.000282461 4 OLA water 1.8015e-05 352 HOH singleParticle particle 10 8.0 Quantifoil R2/2 COPPER 300 CARBON HOLEY ARRAY PLASMA CLEANING 10 AIR

copper grids were first plasma-treated 15 times in EasyGrid,

ETHANE 85 297

Jet vitrified with EasyGrid.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.8 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 6671 1.6 40.3 1 1916000

A first round of blob picking was performed and used to obtain an initial model. this initial model was used to generate templates that were then used to performed template picking, resulting in 1916000 particles

cryoSPARC 4.2 PHASE FLIPPING AND AMPLITUDE CORRECTION 6YC3 C5 2.32 FSC 0.143 CUT-OFF cryoSPARC 4.2 333078 MAXIMUM LIKELIHOOD cryoSPARC 4.2 MAXIMUM LIKELIHOOD cryoSPARC 4.2 100 3000.0 cryoSPARC 4.2 emd_19434.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.47998 268.47998 268.47998 90.0 90.0 90.0 X Y Z -1.2463374 2.2708523 0.0014914346 0.06547618 0.8389999 0.8389999 0.8389999 0.4 AUTHOR ::::EMDATABANK.org::::EMD-19434:::: RIGID BODY FIT REAL emd_19434_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.47998 268.47998 268.47998 90.0 90.0 90.0 X Y Z 0.0 1.0 0.024478363 0.14903715 0.8389999 0.8389999 0.8389999 AUTHOR ::::EMDATABANK.org::::EMD-19434:::: mask for the refinement emd_19434_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.47998 268.47998 268.47998 90.0 90.0 90.0 X Y Z -0.19265793 0.5094958 0.0014914346 0.017058395 0.8389999 0.8389999 0.8389999 AUTHOR ::::EMDATABANK.org::::EMD-19434:::: unsharpened map emd_19434_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.47998 268.47998 268.47998 90.0 90.0 90.0 X Y Z -0.22092775 0.5265573 0.0009716059 0.030415133 0.8389999 0.8389999 0.8389999 AUTHOR ::::EMDATABANK.org::::EMD-19434:::: emd_19434_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.47998 268.47998 268.47998 90.0 90.0 90.0 X Y Z -0.22899713 0.5340844 0.00097013 0.030407393 0.8389999 0.8389999 0.8389999 AUTHOR ::::EMDATABANK.org::::EMD-19434::::