2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2025-04-07 2025-06-25 2025-06-25 2026-08-12 Japan Society for the Promotion of Science (JSPS) 22KJ1795 Japan Japan Society for the Promotion of Science (JSPS) 22H02273 Japan Japan Society for the Promotion of Science (JSPS) 24K08729 Japan Japan Agency for Medical Research and Development (AMED) JP23ama121001 Japan Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, down state Ishikawa-Fukuda M Kishikawa J Kato T Murai M Na+-NQR, Na+ pump, oxidoreductase, MEMBRANE PROTEIN Ishikawa-Fukuda M Seki T Kishikawa JI Takahiro M Okazaki KI Kato T Barquera B Miyoshi H Murai M The Na + -pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from Vibrio cholerae relies on dynamic conformational changes. Biorxiv US 2025 40501732 doi:10.1101/2025.06.01.656757 2692-8205 9ud9 FULLOVERLAP EMDB EMD-64065 associated EM volume
Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, down state
 Na(+)-translocating NADH-quinone reductase Na(+)-translocating NADH-quinone reductase 0 1 2 3 4 5 6 Vibrio cholerae O395 0.214 Na(+)-translocating NADH-quinone reductase subunit A Vibrio cholerae O395 0.048680733999999996 1 Vibrio cholerae LEVO MITIKKGLDLPIAGTPSQVISDGKAIKKVALLGEEYVGMRPTMHVRVGDEVKKAQILFEDKKNPGVKFTSPVSGKVVEIN RGAKRVLQSVVIEVAGDDQVTFDKFEANQLASLNRDAIKTQLVESGLWTAFRTRPFSKVPAIDSTSEAIFVTAMDTNPLA AEPTVVINEQSEAFVAGLDVLSALTTGKVYVCKKGTSLPRSQQPNVEEHVFDGPHPAGLAGTHMHFLYPVSADHVAWSIN YQDVIAVGQLFLTGELYTQRVVSLAGPVVNKPRLVRTVMGASLEQLVDSEIMPGEVRIISGSVLSGTKATGPHAYLGRYH LQVSVLREGRDKELFGWAMPGKNKFSVTRSFLGHLFKGQVYNMTTTTNGSDRSMVPIGNYEKVMPLDMEPTLLLRDLCAG DSDSAVRLGALELDEEDLALCTFVCPGKYEYGQLLRECLDKIEKEG A5F5X1 7.2.1.1 Na(+)-translocating NADH-quinone reductase subunit B Vibrio cholerae O395 0.045390883 1 Vibrio cholerae LEVO MGLKKFLEDIEHHFEPGGKHEKWFALYEAAATLFYTPGLVTKRSSHVRDSVDLKRIMIMVWLAVFPAMFWGMYNAGGQAI AALNHLYSGDQLAAIVAGNWHYWLTEMLGGTMSSDAGWGSKMLLGATYFLPIYATVFIVGGFWEVLFCMVRKHEVNEGFF VTSILFALIVPPTLPLWQAALGITFGVVVAKEVFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVWTAADGYSGATALSQ WAQGGAGALINNATGQTITWMDAFIGNIPGSIGEVSTLALMIGAAFIVYMGIASWRIIGGVMIGMILLSTLFNVIGSDTN AMFNMPWHWHLVLGGFAFGMFFMATDPVSASFTNSGKWAYGILIGVMCVLIRVVNPAYPEGMMLAILFANLFAPLFDHVV VERNIKRRLARYGKQ A5F5X0 7.2.1.1 Na(+)-translocating NADH-quinone reductase subunit C Vibrio cholerae O395 0.02765227 1 Vibrio cholerae LEVO MASNNDSIKKTLFVVIALSLVCSIIVSAAAVGLRDKQKENAALDKQSKILQVAGIEAKGSKQIVELFNKSIEPRLVDFNT GDFVEGDAANYDQRKAAKEASESIKLTAEQDKAKIQRRANVGVVYLVKDGDKTSKVILPVHGNGLWSMMYAFVAVETDGN TVSGLTYYEQGETPGLGGEVENPAWRAQWVGKKLFDENHKPAIKIVKGGAPQGSEHGVDGLSGATLTSNGVQNTFDFWLG DMGFGPFLTKVRDGGLN A5F5Y7 7.2.1.1 Na(+)-translocating NADH-quinone reductase subunit D Vibrio cholerae O395 0.022853217 1 Vibrio cholerae LEVO MSSAKELKKSVLAPVLDNNPIALQVLGVCSALAVTTKLETAFVMTLAVMFVTALSNFFVSLIRNHIPNSVRIIVQMAIIA SLVIVVDQILKAYLYDISKQLSVFVGLIITNCIVMGRAEAFAMKSEPIPSFIDGIGNGLGYGFVLMTVGFFRELLGSGKL FGLEVLPLISNGGWYQPNGLMLLAPSAFFLIGFMIWAIRTFKPEQVEAKE A5F5Y6 7.2.1.1 Na(+)-translocating NADH-quinone reductase subunit E Vibrio cholerae O395 0.021481678 1 Vibrio cholerae LEVO MEHYISLLVKSIFIENMALSFFLGMCTFLAVSKKVKTSFGLGIAVIVVLTISVPVNNLVYNLVLKPDALVEGVDLSFLNF ITFIGVIAALVQILEMILDRFFPPLYNALGIFLPLITVNCAIFGGVSFMVQRDYSFAESVVYGFGSGVGWMLAIVALAGI REKMKYSDVPPGLRGLGITFITAGLMALGFMSFSGVQL A5F5Y5 7.2.1.1 Na(+)-translocating NADH-quinone reductase subunit F Vibrio cholerae O395 0.04594236299999999
C-TERMINAL INCLUDES HIS-TAG SEQUENCE AS A PURIFICATION TAG.
1 Vibrio cholerae LEVO MSTIIFGVVMFTLIILALVLVILFAKSKLVPTGDITISINGDPEKAIVTQPGGKLLTALAGAGVFVSSACGGGGSCGQCR VKIKSGGGDILPTELDHISKGEAREGERLACQVAVKADMDLELPEEIFGVKKWECTVISNDNKATFIKELKLAIPDGESV PFRAGGYIQIEAPAHHVKYADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNVRIATPPPNNPNV PPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYV EDFDGLAAENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMCGPPMMNAAVINMLKNLGVEEEN ILLDDFGGHHHHHH A5F5Y4 7.2.1.1 FLAVIN MONONUCLEOTIDE 0.00045634399999999997 2 FMN RIBOFLAVIN 0.00037636399999999996 1 RBF CALCIUM ION 4.0078e-05 1 CA FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES FLAVIN-ADENINE DINUCLEOTIDE 0.0007855499999999999 1 FAD water 1.8015e-05 2 HOH singleParticle particle 10 8.0 50.0 C4H13Cl2NO3 Tris-HCl 1.0 C10H16N2O8 Ethylenediaminetetraacetic acid 0.05 C24H46O11 n-DODECYL-beta-D-MALTOSIDE 5.0 C21H27N7O14P2 NADH Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.035 0.8 1.8 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Image corrector GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 65.0 1
Non-uniform refinement
3653368 cryoSPARC v3.3.1 NONE 7XK3 C1 FOURIER SPACE 3.11 FSC 0.143 CUT-OFF cryoSPARC v3.3.1 77726 MAXIMUM LIKELIHOOD cryoSPARC v3.3.1 MAXIMUM LIKELIHOOD cryoSPARC v3.3.1 4 cryoSPARC v3.3.1 emd_64065.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.7860639 1.3096958 0.00010170381 0.03259126 0.88 0.88 0.88 0.149 AUTHOR 7XK3 PDB experimental model FLEXIBLE FIT REAL emd_64065_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.009314727 0.019549051 0.00006335882 0.00060801016 0.88 0.88 0.88 AUTHOR emd_64065_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.46667108 0.7585289 0.0006535061 0.0465065 0.88 0.88 0.88 AUTHOR emd_64065_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -0.44886786 0.73877203 0.00065395335 0.04648459 0.88 0.88 0.88 AUTHOR