2024-11-06 REL RCSB RCSB RCSB 2018-12-10 2019-01-23 2019-02-27 2024-11-06 Department of Energy (DOE, United States) DE-AC02-O5CH11231 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 5T32GM007232-38 United States Department of Energy (DOE, United States) DE-SC00016240 United States T.elongatus NDH (data-set 2) Laughlin TG Bayne A photosynthesis, bioenergetics, membrane protein complex, OXIDOREDUCTASE Laughlin TG Bayne AN Trempe JF Savage DF Davies KM Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Nature UK 566 411 414 2019 30742075 doi:10.1038/s41586-019-0921-0 1476-4687 0006 NATUAS EMD-0415 other EM volume EMD-0416 other EM volume EMD-0417 other EM volume EMD-0418 other EM volume EMD-0419 other EM volume EMD-0420 other EM volume 6nbx FULLOVERLAP NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus 0 1 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17 18 Thermosynechococcus elongatus BP-1 0.42 NAD(P)H-quinone oxidoreductase subunit 1 Thermosynechococcus elongatus (strain BP-1) BP-1 0.04056598399999999 1 LEVO MESGIDLQGQFISALQSLGLSHDLAKLLWLPLPMLMMLIVATVGVLVAVWLERKISAAVQQRIGPEYIGPLGILAPLADG LKLIFKEDVLPANSDRWLFTLGPAVVVIPVFLSYIIVPFGQNLLISNLAMGVFLWIALSSIAPIGLLMAGYASNNKYSLL GGLRAAAQSISYEIPLALAVLAVAMMSNGLGTVEIVEQQSQYGILSWNVWRQPIGFLVFWIAALAECERLPFDLPEAEEE LVAGYQTEYAGMKFALFYLGAYVNLVLSALLVSVLYFGGWSFPIPLETIANLLGVSETNPFLQIAFAVLGITMTLIKAYF FVFLAILLRWTVPRVRIDQLLDLGWKFLLPVGLVNLLLTAGLKLAFPVAFGG Q8DL32 7.1.1.- NAD(P)H-quinone oxidoreductase subunit 2 Thermosynechococcus elongatus (strain BP-1) BP-1 0.055168542999999994 1 LEVO MDLVTLAGQLNAGTILPETILIVTLLVVLLADLIQGRQADRWTPYFAIVGLGGAIATMIPLWTQPATISFFGSFISDHLS LFFRGLIALSALGTILMSIRYVEQTGSSLGEFMTILLTATVGGMFIAGAQELVFIFVALETLSIASYLLTGYTKRDSRSN EAALKYLLIGAASSAIFLYGSSLLYGLSGGHTQLPAIAQALSSESLGLVVALVFVIAGISFKISAVPFHQWTPDVYEGAP TPVVAFLSVGSKAAGFALAIRFLTLAFPSVTDQWQLIFTVLAILSMILGNVVALAQTSMKRMLAYSSIGQAGFVMIGFVV GTEAGYASMLFYLLVYLFMNLGAFTCVILFSLRTGTDQISEYAGLYQKDPLLTLGLSLCLLSLGGIPPLAGFFGKIYLFW AGWQAGAYGLVLLGLLTSVISIYYYIRVVKMMVVKEPQEMSEAVRNYPEVSWSSFGLRPLQVGLVMTVIATSLAGILANP LFNLVNTAVWDVPQLANQPTVMEVAYQALSPAGKS Q8DMR6 7.1.1.- NAD(P)H-quinone oxidoreductase subunit 3 Thermosynechococcus elongatus (strain BP-1) BP-1 0.015013918999999999 1 LEVO MVAIPRLRDTATVFVLSGYEYFLGFLIICSLVPVLALAASALLRPKSGRMIRLTTYESGMEPIGGAWIQFNVRYYMFALV FVIFDVETVFLYPWAVAFHQLGLLAFIEALIFIAILVVALVYAWRKRALEWS Q8DJ02 7.1.1.- NAD(P)H-quinone oxidoreductase chain 4 1 Thermosynechococcus elongatus (strain BP-1) BP-1 0.057847504 1 LEVO MSTFPWLTTIILFPIVAALAIPFIPDPTGKGRPIRWYALAVGLIDFALIVYAFTNFYDLNTPGMQLWESYDWIPEIGLRW SVGADGLSMPLILLTGFITTLAILAAWPVTLKPRLFYFLMLAMYGGQIAVFAVQDMLVFFLAWELELIPVYLLLAIWGGH KRQYAATKFILYTAGSSLFILVAGLAMAFYGDTVSFDMQTLAAKDYALGFQLLVYAGFLVAYGVKLPIVPLHTWLPDAHG EATAPVHMLLAGILLKMGGYALIRMNVDMLPAAHAKFAPVLVILGVVNIIYAALTSYAQRNLKRKIAYSSISHIGFVLIG IASFTNLGMSGAVLQMVSHGLIGASLFFLVGATYDRTHTLILEEMGGVGQKMKKIFAMFTACSLASLALPGMSGFVAELM VFIGFATSDAYSLPFRVIVVFLAAVGVILTPIYLLSMLREIFYGPENKELVEHEALVDAEPREVFIIACLLVPIIGIGLY PKLLTQIYDATTGQVIARAREVLPTLAQQTEQPLGILPMVAPQLKANAQ Q8DKY0 1.6.5.- NAD(P)H-quinone oxidoreductase subunit 4L Thermosynechococcus elongatus (strain BP-1) BP-1 0.011140264999999998 1 LEVO MQLTYVLILAALLFCIGIYGLVTSRNAVRVLMSIELLLNAVNLNLIGFANYLDGQQIKGQVFAVFVITVAAAEAAVGLAI ILAIYRNRDTVDMEKFNLLKW Q8DL29 1.6.5.- NADH dehydrogenase subunit 5 Thermosynechococcus elongatus (strain BP-1) BP-1 0.072025352 1 LEVO MEPLYQYAWLIPVLPLLGALIVGFGLIAFSETTSKLRRPSAIFIMALMAIAMGHSLTLFWSQVQGHLPYTQMIEWAAAGN LHIAMGYVIDPLAALMLVIVTTVAFLVMLYSDGYMAHDPGYVRFFAYLSLFGSSMLGLVVSPNLVQVYIFWELVGMCSYL LIGFWYDRKSAAEAAQKAFVTNRVGDFGLLLGMVGLFWATGTFDFAGMGDRLTELVNTGLLSPSLAAILAILVFLGPVAK SAQFPLHVWLPDAMEGPTPISALIHAATMVAAGVFLIARMFPVFEQLPQVMTTIAWTGAFTAFMGATIAITQNDIKKSLA YSTISQLGYMVMGMGVGAYSAGLFHLMTHAYFKAMLFLGSGSVIHSMEGVVGHNPDLAQDMRYMGGLRKYMPITGATFLV GCLAISGVPPFAGFWSKDEILGAVFHANPAMWLLTWLTAGLTAFYMFRMYFMTFEGKFRNVPPERQEHHDHHSHHAAVPH ESPWTMTLPLVVLAIPSTLIGFVGTPFNNLFEVFIHAPGEEKVAEHAVDLTEFLILGGSSVGIGLMGITVAYLMYLKGTP SPQAIAKAIQPLYQFSLHKWYFDELYEAVFIKGCRRLARQVLEVDYNVVDGVVNLTGFVTMVTGEGLKYLQNGRAQFYAL IVLLAVLGFVIFSVQT Q8DKX9 NADH-quinone oxidoreductase subunit J Thermosynechococcus elongatus (strain BP-1) BP-1 0.021580567999999998 1 LEVO MDLATLTQTITFFALAAAVIIAALGVVLLDNVVYSAFLLGGVFLSIAGLYILMNADFVSAAQILIYVGAVNVLILFAIML VNKRETYTPVPGRWLRQGGAAVVSLGVFALLTKMILQTPWQLSSVPPTPDSITTIGQHFFSDFLLPFELASVLLLMALIG AVVLARRELVLEPEPILGEEVVPPLELPERPREPVALSEK Q8DL30 1.6.5.11 NAD(P)H-quinone oxidoreductase subunit H Thermosynechococcus elongatus (strain BP-1) BP-1 0.045271184 1 LEVO MPKIETRTEPMVINMGPHHPSMHGVLRLMVTLDGEDVIDCEPVIGYLHRGMEKIAENRTNIMFIPYVSRWDYAAGMFNEA VTVNAPEKLAGIPVPKRASYIRVIMLELNRIANHLLWLGPFLADVGAQTPFFYIFREREYIYDLFEAATGMRFINNNYFR IGGVAADLTYGWVTKCRDFCDYFLPKVDEYERLITNNPIFVRRLQGVGKISREEAINWGLSGPMLRASGVKWDLRKVDHY ECYDDFDWDVPVATEGDCLARYIVRIQEMRESVKIIRQALDGLPGGPYENLEAKRMLEGAKSEWNGFDYQYIGKKLSPTF KIPKGEHYVRVESGKGELGIYLIGDDNVFPWRWKIRPPDFNNLQVLPQLLKGMKVADIVAILGSIDVIMGSVDR Q8DJD9 1.6.5.- NAD(P)H-quinone oxidoreductase subunit I Thermosynechococcus elongatus (strain BP-1) BP-1 0.022444800999999997 1 LEVO MKFLNQITNYAKEAVQSAKYIGQGLSVTFDHMRRRPITVQYPYEKLIPSERFRGRIHFEFDKCIACEVCVRVCPINLPVV DWVFNKELKKKELKHYSIDFGVCIFCANCVEYCPTNCLSVTEEYELATYDRHELNYDSVAMGRIPYKVTQDPMVTPIREF AYLPAGVMSGHDLPAGAQRAGERPEAIANTAKSSEN Q8DL31 1.6.5.- NAD(P)H-quinone oxidoreductase subunit J Thermosynechococcus elongatus (strain BP-1) BP-1 0.019363789 1 LEVO MSDTPEAPIVEAGPVGRLLQSQNLSVESLGRDASGVEMIKVDRDRLLAVCQTLYADGFNYLRCQAAYDSGPGQDLVSTYH LIKLSDNADRPPEVRIKVFVPRDDPRVPSVYWIWKTADWQERESYDMFGIVYEGHPNLKRILMPEDWVGWPLRKDYITPD FYELQEAY Q8DJ01 1.6.5.- NAD(P)H-quinone oxidoreductase subunit K Thermosynechococcus elongatus (strain BP-1) BP-1 0.025766998 1 LEVO MTNTTSPAILNPIARPEVPQELAENIILTSLNDVYDWARLSSLWPLMYGTACCFIEFAAMIGSRFDFDRFGLVPRNSPRQ ADLIITSGTITMKMAPALVRLYEQMPSPKYVIAMGACTITGGMFSSDSYSAVRGVDKLIPVDVYLPGCPPRPEAIMDAIV KLRKKIANEHINERGNLAQTHRLFTAKHKMKPVPPILTGQYLNAPSRQAPPPALAAAMGIAVPALGEAVSETTSVAE Q8DKZ4 1.6.5.- NAD(P)H-quinone oxidoreductase subunit L Thermosynechococcus elongatus (strain BP-1) BP-1 0.008575137 1 LEVO MAVSTELLVLGVYGALAGLYLLVVPAIVYAYLNARWYVASSFERAFMYFLVTFFFPGLLLLAPFINFRPQPRSLNS Q8DKZ3 1.6.5.- NAD(P)H-quinone oxidoreductase subunit M Thermosynechococcus elongatus (strain BP-1) BP-1 0.012584056 1 LEVO MLLKSTTRHVHIYAGHVVDGEVHPDTETLTLNVDPDNELEWNEAALAKVEAKFRELVANAAGEDLTEYNLRRIGSDLEHF IRSLLMQGEIGYNLNSRVRNYSLGIPRVNHS Q8DLN5 1.6.5.- NAD(P)H-quinone oxidoreductase subunit N Thermosynechococcus elongatus (strain BP-1) BP-1 0.016656182 1 LEVO MGLLAGYQFVKDLESAGALALFVPPEGGFEGRYQRRLRSKGYTTLPMSAPGLGDLAAYLTQEHGIRPAHTGKEDIRVYFQ PPLVTYHLENLPPNAKGLVLWLIDGKRLSKQEFAYLAQLTQTLPKFKVVVEVGGDRVVRWEPLADWVAAA Q8DJU2 1.6.5.- NAD(P)H-quinone oxidoreductase subunit O Thermosynechococcus elongatus (strain BP-1) BP-1 0.007877076 1 LEVO MAIKKGDLVKVVAEKLANSLEALASDHRYPPYLFEGRGEVVDIRGDYAQIKFPVPTPTVWLRLDQLEVAQ Q8DMU4 1.6.5.- Proton-translocating NADH-quinone dehydrogenase subunit P NdhP Thermosynechococcus elongatus (strain BP-1) BP-1 0.0048786490000000005 1 LEVO MDAVISVKPILLAMTPVFILLCLFFGTRNGFYDTDQYHGNGSAH V5V507 Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ Thermosynechococcus elongatus (strain BP-1) BP-1 0.004844698 1 LEVO MATDFNRGIMKFDGADSPAMIAISAVLILGFIAGLIWWALHTAYA Tlr0636 protein Thermosynechococcus elongatus (strain BP-1) BP-1 0.012462558999999998 1 LEVO MIRPIADTYPLLPLSKAQMGQRQEIINSHKRLWDKTMATDLIMTILPGMTVKVTNPNDTYYQFQGIVQRITDGKVAVLFE GGNWDKLVTFQASELEPVVVTPKEKAKAKK Q8DL61 IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 singleParticle particle 0.03 6.0 20.0 Bis-Tris 100.0 sodium chloride 0.03 B-dodecyl-maltoside Quantifoil R2/2 COPPER 300 CARBON CONTINUOUS 7.0 GLOW DISCHARGE OTHER ETHANE 100 295 FEI VITROBOT MARK IV
incubate on grid for 30 seconds and blot 2.5 seconds before plunging.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 25 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1-30 1 1385 0.2 60.0
Three image per hole, focusing once per hole.
 1
Super-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
98145
Ab initio from cryoSPARC
 C1 BACK PROJECTION 3.5 FSC 0.143 CUT-OFF RELION 3.0.b2 34655 MAXIMUM LIKELIHOOD RELION 3.0.b2 MAXIMUM LIKELIHOOD RELION 3.0.b2 emd_0425.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 384.47998 384.47998 384.47998 90.0 90.0 90.0 X Y Z -14.495347000000001 41.702187000000002 -0.0021918472 0.8420073 1.068 1.068 1.068 5.5 AUTHOR pixel spacing resized to match EMD-415 6NBQ PDB experimental model RIGID BODY FIT Corelation coefficient REAL 20.0 emd_0425_msk_1.map emd_0425_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 403.91998 403.91998 403.91998 90.0 90.0 90.0 X Y Z -0.08144294 0.13686927 0.000007264483 0.008415058 1.122 1.122 1.122 AUTHOR binned relative to original particle images emd_0425_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 403.91998 403.91998 403.91998 90.0 90.0 90.0 X Y Z -0.081906736 0.16600402 0.000011284295 0.008128974 1.122 1.122 1.122 AUTHOR em-half-volume_P2