2025-12-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-11-19 2025-12-17 2025-12-17 2025-12-17 Swiss National Science Foundation TMCG-2+213773 Switzerland Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the O2 state Haubner M Williams HM Hruby J Straub MS Guskov A Kovalev K Drabbels M Lorenz UJ rhodopsin, ErNaR, sodium pump, phototransduction, MEMBRANE PROTEIN Haubner M Williams HM Hruby J Straub MS Guskov A Kovalev K Drabbels M Lorenz UJ Microsecond Time-Resolved Cryo-EM Based on Jet Vitrification. Biorxiv US 2025 41332690 doi:10.1101/2025.11.21.689681 2692-8205 EMD-55761 other EM volume
different protein, same paper
 EMD-55765 other EM volume
same protein, same paper
 EMD-55766 other EM volume
same protein, same paper
 9tbf FULLOVERLAP EMDB EMD-55761 other EM volume
different protein, same paper
 EMDB EMD-55765 other EM volume
same protein, same paper
 EMDB EMD-55766 other EM volume
same protein, same paper
 EMDB EMD-55769 associated EM volume
Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the O2 state
 PDB 9TBD unspecified
same protein, same paper
 PDB 9TBE unspecified
same protein, same paper
 ErNaR light-driven sodium pump ErNaR light-driven sodium pump 0 1 Erythrobacter Bacteriorhodopsin-like protein Erythrobacter 0.030676467
Bear in mind that LFA and LMT are not part of the sequence here. They derive from the protein solution.
1 Escherichia coli LEVO MPSIENFLAYDFWQYDVIRHLFAFSTAVFLAGLVYFAMTARTTAPNYRLSANISAVVMVSAALELGQLWLLWNESFQWAE LQGSFVPVAGERFSNGYRYMNWLIDVPMLATQLVVVCGFVGTELRNRWAKLTIAGVLMILTGYVGQYFEPAVAGVPGYEG AEQFWIWGIISTAFFVWMLLILANAVRNPQGAPSDEVRSRLKFCFWFLLATWSIYPFAYAMPLFAPTADGVVVRQVIYTV ADVSSKLVFGVILSQVALRRSAEEGFEPARVASG EICOSANE 0.000282547 10 LFA DODECYL-BETA-D-MALTOSIDE 0.000510615 3 LMT RETINAL 0.00028443599999999994 1 RET water 1.8015e-05 13 HOH singleParticle particle 4.5 8.0 500.0 NaCl sodium chloride 10.0 C4H11NO3 Tris-HCl 0.04 C24H46O n-dodecyl-beta-D-maltoside (DDM)
10 mM HEPES pH 7.5, 500 mM NaCl
 Quantifoil R1.2/1.3 GOLD 200 GLOW DISCHARGE AIR
Grid was sputter coated with 40 nm thick layer of silver beforehand using a Quorum Q300T device.
 ETHANE 95 277 FEI VITROBOT MARK IV
Vitrification carried out using a modified Vitrobot Mark IV, as outlined in the paper reporting this entry..
This sample was monodisperse.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.4 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 40.0 1 cryoSPARC 4.6.0 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.3 FSC 0.143 CUT-OFF cryoSPARC 4.6.0
Reconstruction conducted in C1 following symmetry expansion of particle stack in C5.
67385 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_55769.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 278.784 278.784 278.784 90.0 90.0 90.0 X Y Z -0.5570916 0.6757173 0.00035737595 0.010196438 0.726 0.726 0.726 0.12 AUTHOR Sharpened consensus map emd_55769_msk_1.map emd_55769_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 278.784 278.784 278.784 90.0 90.0 90.0 X Y Z -0.20955697 0.23380643 0.0001974128 0.025915885 0.726 0.726 0.726 AUTHOR Half map A emd_55769_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 278.784 278.784 278.784 90.0 90.0 90.0 X Y Z -0.24317043 0.22539209 0.00019820107 0.025992824 0.726 0.726 0.726 AUTHOR Half map B