Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi

2023-08-23 REL PDBe PDBe PDBe 2022-10-18 2023-08-09 2023-08-09 2023-08-23 Israel Science Foundation 199/21 Israel Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi Fadeeva M Klaiman D Caspy I Nelson N Green alga, PSII, C.ohadi, membrane protein, Cryo-EM, PHOTOSYNTHESIS Fadeeva M Klaiman D Caspy I Nelson N Structure of Chlorella ohadii Photosystem II Reveals Protective Mechanisms against Environmental Stress. Cells CH 12 2023 37566050 doi:10.3390/cells12151971 2073-4409 8bd3 FULLOVERLAP Chlorella ohadii Photosystem II Chlorella ohadii Photosystem II 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Chlorella ohadii Chloroplast Thylakoid membrane 1.7 Chlorophyll a-b binding protein, chloroplastic Chlorella ohadii 0.023060059 2 LEVO SQWYGPDRPKFLGPYSTNFVPSYLTGEFPGDYGWDTSGLSADPATFARYREIEVIHARWAMLGALGCVVPELLDGTNHIA WFKAGAEIFGDDGIQYLGIPGLINAKSIVATLIVQVVLMSYVEGYRVNGGPAGTGLDAVYPGGNFDPLGLADDPDTLAEL KVKEIKNGRLAMLSMFGFFIQAIVTGEGPIKNLNDHLADASANNFYALYAKNLA A0A2P6TPU9 Chlorophyll a-b binding protein, chloroplastic Chlorella ohadii 0.023850741999999998 6 LEVO EFYGPDRAKWLGPFSEGSVPSYLKGEFPGDYGWDTAGLSADPETFARYREIEVIHARWAMLGALGCLTPELLQNNGAADF GEAAVWFKAGASIFNEDGLNYLGNPSLIHAQSIVAVLLTQLVIMGAAEAYRYSGEGPVETSGDSLYPGGFFDPLGLADDP DTLAELKVKEIKNGRLAMFSMFGFFVQGLVTGKSPLENLADHLAEPSVNNGFASATKFLPLP A0A2P6TDA6 Chlorophyll a-b binding of LHCII Chlorella ohadii 0.023847945 6 LEVO VEWYGPNRPQFLGPFSNPPSYLKGEFPGDYGWDTAGLSADPETFARYRELEVIHARWAMLGALGCVTPELLQRNGVANFG EAVWFKAGAQIFQEGGLDYLGNPSLIHAQSIVAILLTQLVLMGLIEGYRVNGGPAGEGLDALYPGEAFDPLGLADDPDTF AELKVKELKNGRLAMVSMLGFGVQGLITRKGPIENLADHLAAPDATNFWVDYAPKSAGIGY Chlorophyll a-b binding of LHCII Chlorella ohadii 0.02345549 2 LEVO EFYGPDRVKFLGPFSGNTPSYLKGEYPGDYGWDTAGLSADPETFARYRELEVIHARWAMLGALGCVTPELLQRNGAANFG EAVWFKAGAQIFQEGGLDYLGNPNLVHAQSIVAILLTQVVLMGLIEGYRVNGGPAGEVVDPIYPGEAFDPLGLADDPDTL AELKVKEIKNGRLAMVSMFGFFIQAIVTGKGPVQNLSDHLASPSTDNFYSLYAKTLA Photosystem II protein D1 Chlorella ohadii 1 0.03723032 2 LEVO ESTSLWARFCEWVTSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAIIPTSNA IGLHFYPIWEAASLDEWLYNGGPYQLIVCHFFLGVCSYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFIIYPLGQGSF SDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYKFGQEEETYNI VAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGFNFNQSVVDSQGRVINTWADIINRANLGM EVMHERNAHNFPLDLA W8SIR2 Photosystem II CP47 reaction center protein Chlorella ohadii 0.055754269999999995 2 LEVO GLPWYRVHTVVLNDPGRLIAVHLMHTSLVSGWAGSMAFYELAVFDPSDPVLNPMWRQGMFVLPFMTRLGITQSWGGWTIS GETASNPGIWSYEGVAAAHIILSGLLFAASIWHWVYWDLELFRDPRTSNPALDLPKIFGIHLFLSGLLCFGFGAFHVTGL FGPGIWVSDPYGITGTVQAVAPSWDATGFDPYNPGGISAHHIAAGILGVLAGLFHLCVRPPQRLYNGLRMGNIETVLSSS IAAVFWAAFVVSGTMWYGSAATPIELFGPTRYQWDLGFFQQEIERRVQTSLAEGKSASQAWAEIPEKLAFYDYIGNNPAK GGLFRAGAMNSGDGIAVGWLGHAVFKDKQGNELFVRRMPTFFETFPVVLLDKDGVVRADVPFRRSESKYSIEQVGVSVTF YGGELDGVTFSDPATVKKYARRAQLGEIFEFDRATLQSDGVFRTSPRGWFTFAHLCFALLFFFGHIWHGARTIFRDVFAG IDADLDEQVEFGAFLKLGDTSTRR W8TIK4 Photosystem II CP43 reaction center protein Chlorella ohadii 0.049161105000000004 2 LEVO GRDQESTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVAHFVPEKPMYEQGLILLPHLATLGYGVGPGGE VIDTYPYFVSGVLHLISSAVLGFGGVYHSLVGPETLEESFPFFGYVWKDKNKMTTILGIHLIVLGLGAWLLVWKAMYFGG IYDTWAPGGGDVRIITNPTVSPGVIFGYLFRSPFGGDGWIVSVDNMEDVIGGHIWIGTLCIFGGIWHILTKPWAWARRAF VWSGEAYLSYSLGAISIMGFTACCMAWFNTTAYPSEFYGPTGPEASQSQTFTFLVRDQRLGANVASAQGPTGLGKYLMRS PTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKLKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINAVNYVSPRS WLATSHFCLGFFFFVGHLWHAGRARAAAAGFEKGIDRDNEPVLSMRPL A0A076EAP1 Photosystem II D2 protein Chlorella ohadii 0.038459944999999995 2 LEVO KRGWFDVVDDWLRRDRFVFVGWSGLLLFPTAYLALGGWFTGTTFVTSWYTHGLASSYLEGCNFLTAAVSTPANSMGHSLL FLWGPEAQGDFTRWCQLGGLWTFVALHGSFSLIGFMLRQFEIARSVKIRPYNAIAFSAPISVFVSVFLIYPLGQSGWFFA PSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQAEETYSMVTAN RFWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMA AQDQPHEKLVFPEEVLPRGNAL W8SYD4 Cytochrome b559 subunit alpha Chlorella ohadii 0.009204326999999998 2 LEVO SGATGERPFSDILTSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTEDRQETPLITDRFNALEQVKKLSE V W8SU91 Cytochrome b559 subunit beta Chlorella ohadii 0.004262068 2 LEVO KSYTYPIFTVRWLAVHALAVPTVFFLGAITAMQFIQR P56310 Photosystem II reaction center protein H Chlorella ohadii 0.007223423 2 LEVO DTGISTPLGTLLKPLNSEYGKVAPGWGTTVLMGIFMALFAVFLVIILEIYNSSVLLDDVTMSWESLA W8SIT0 Photosystem II reaction center protein I Chlorella ohadii 0.003871545 2 LEVO MLTLKIFVYTVVTFFVSLFIFGFLSNDPGRNPGQ A0A5P4ND48 Photosystem II reaction center protein J Chlorella ohadii 0.0038134679999999995 2 LEVO GTTGRIPLWLVGTVAGVAVIALVGIFFYGSYVGLGSSL W8TIH6 Photosystem II reaction center protein K Chlorella ohadii 0.004139957999999999 2 LEVO KLPEAYAPFDPIVDVLPVIPVLFLLLALVWQASVSFR P56348 Photosystem II reaction center protein L Chlorella ohadii 0.0042599660000000004 2 LEVO AKPNPNKQSVELNRTSLYWGLLLIFVLAVLFSSYIFN P56339 Photosystem II reaction center protein M Chlorella ohadii 0.005621872 2 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)MEVNILGVIATALFIIIPTSFLLILYVKTASQ A0A5P4NAV9 Chloroplast oxygen-evolving enhancer protein 1 Chlorella ohadii 0.025449529 2 LEVO LTFDQLQGLTYLQVKGTGIANTCPTLDSGSSNVKDLKPGTYKLGKFCMEPTSFTVKEESQFKGGDAEFVPTKLMTRLTYT LDEMSGQFKVDGSGNVELKETDGIDYAPVTVQLPGGERVPFLFSVKELDAKGNADGFGGEFVVPSYRGATFLDPKGRGAA TGYDTAVALPAAGDDEEYLKENIKSAGAMKGQAVFSIAKVDAATGEIAGVFESVQPSDTDLGAKAPKDVKITGLWYAQLS A0A5P4NF37 Chlorophyll a b binding CP29 Chlorella ohadii 0.025803734 2 LEVO RSGGAGYRQYSGDALWLPNTERPAWLDGSLPGDRGFDPLGLSRPAEYLQIDLDELDQNAAVNKAGGVVGAFTPVADQVST DSLAPYSEVFGLQRFRECELIHGRWAMLACLGALVQEGVTGDSWVAAQTLVYNQPQYAGIDLPFDIYTLAVLNSVLMGGV ELFRNSELDPERR(CSU)YPGGAFDPLNLASDDSERTQKLREAEIKHARLAMVSFLGYTVQAWYTGEGALGSLNKFANGF Chlorophyll a b-binding CP26 Chlorella ohadii 0.027369807 2 LEVO VSRSGGWLGSDSQNINLDKWYGPDRVLYLPGGLLARDEINPVLNGTLPGDYGYDPLGLAKDAETLAKYRANELLHARWAM LAAAGAIIPEGLAANGADVKGATWFETGAAMLNGGTLNWFAVPFVNFNNPLPLFAVVAINVALMAAAENYRRTEDGPAGY APGVGKFDESVYSNMDNLYPGGPFDPLGLADDPEVLAELKVKEIKNGRLAMVSFLGFAVQAAVTGEGPYANWSKHVADPF GYNLLTILSSEDRAAVL Photosystem II reaction center protein T Chlorella ohadii 0.0034762199999999995 2 LEVO MEALVYTFLLVGTLGIIFFAIFFREPPRIV P56327 Photosystem II reaction center protein Ycf12 Chlorella ohadii 0.0033190100000000003 2 LEVO NLEIVLQLTALLFIVAAGPLVIVLLSSRGGNL A0A076EAR3 Photosystem II reaction center W protein Chlorella ohadii 0.00662335 2 LEVO LVDDRLAGEGTGKILGINDPSLFWAITIVFTIVWGVFYVSTREIDAASDRENDDDFGLTL Photosystem II reaction center protein X Chlorella ohadii 0.0035260279999999996 2 LEVO AATPSLNNLIGSVVAGGLVLAAIAGAITAVSNFDSIR Multifunctional fusion protein Chlorella ohadii 0.023863996 2 LEVO VWYGPDRPKFLGPFSDGLVPAYLTGEFPGDYGWDTSGLSADPETFKKYRTIEVIHARWAMLGALGCIFPEVLEKYSGVQF GEAVWFKAGAQIFADGGLNYLGNSGLVHAQSIVATLVVQVLLMGAVEIYRANGEGPNGFGEGQDTLYPGGAFDPLGLADD PDTLAELKVKEIKNGRLAMLSMLGFFVQAIVTGKGPLDNLLQHLEEPGEFNFYALYANSLA A0A2P6U5M3 2.7.1.107 Photosystem II reaction center protein Z Chlorella ohadii 0.006727146999999999 2 LEVO MLLIFQLALFAFIVVSFLLVVGVPVVLATPEGWAENKGTVFSGIGIWFLLVFLVGILNSFVV W8SKL0 Chloroplast oxygen-evolving enhancer protein 3 Chlorella ohadii 0.015948137 2 LEVO LDLFDDRKARQAGFDIIYEARDLDLPQGVRDGLAQARENLDVAKARIKEAEKRIDADLDAYIAKAYWTEGRNELRRQVGT LRFDLNAVADTLPKAAKKEAQAAKNEFLAAVEALDLQLRKKNGDKAAAALADTKAKLDAVIAKL A0A5P4NB29 Chloroplast PsbY Chlorella ohadii 0.003697331 2 LEVO DNRFGTIALLAVPVIGWVLFNILGPLQNQLNAMS A0A5P4NEE0 Chloroplast photosystem II 10 kDa protein Chlorella ohadii 0.011657287 2 LEVO KIDISKQGLNSIQNETVKLNLMGKSKTMESKDWVDPQGRKGKGYGVYRFANKYGANVDGYSPIYTPDTWSESGDSYKLGT KGLIAWAGLIVVLLGVGINLVISTSALG A0A5P4NAS4 Photosystem II oxygen evolving enhancer 2 Chlorella ohadii 0.020416791 2 LEVO AYGDAARVFAGNITNKSGFIPYAGEGFALLIPSKWNPSKEQDFPGVVLRYEDNGDAVNNLVVLVQKVGKNNIDELGSPDK FLQDNAYLFGESAAFTGETLSEGGFLPNKVAAASVLDVQEATDKKGKKYYKYEVLTRSADGDEGGRHQLIAATVSNGNLY LIKVQCGDKRWFKGAKREAIGAWDSFTV CHLOROPHYLL B 0.000907472 122 CHL CHLOROPHYLL A 0.000893489 270 CLA (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 36 LUT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 44 LHG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 86 LMG (3R)-beta,beta-caroten-3-ol 0.0005528719999999999 6 RRX (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL 0.00060087 22 NEX (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.00060087 8 XAT 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 24 SQD CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX FE (II) ION 5.5845e-05 2 FE2 CHLORIDE ION 3.5453e-05 4 CL PHEOPHYTIN A 0.0008712 4 PHO BETA-CAROTENE 0.000536873 22 BCR 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE 0.000749201 4 PL9 DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 8 DGD BICARBONATE ION 6.1017e-05 2 BCT PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM DODECYL-ALPHA-D-MALTOSIDE 0.000510615 4 LMU water 1.8015e-05 224 HOH singleParticle particle 4 6.0

20 mM MES NaOH pH 6 0.1% alfaDM

Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 12.0 PLASMA CLEANING 40 AIR ETHANE 95 293 LEICA EM GP FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 1.8 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 (6k x 4k) 21341 50.0 1 734768 8 C1 2.73 FSC 0.143 CUT-OFF 94893 OTHER 10 12000.0 emd_15973.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 460.8 460.8 460.8 90.0 90.0 90.0 X Y Z -0.027582256 0.066376135 0.00021178843 0.0023458973 0.9216 0.9216 0.9216 0.008 AUTHOR ::::EMDATABANK.org::::EMD-15973:::: emd_15973_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 460.8 460.8 460.8 90.0 90.0 90.0 X Y Z -0.016115937 0.036873218 0.00021180863 0.0018613245 0.9216 0.9216 0.9216 AUTHOR ::::EMDATABANK.org::::EMD-15973:::: emd_15973_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 460.8 460.8 460.8 90.0 90.0 90.0 X Y Z -0.015228821 0.037772316 0.00021176806 0.0018607323 0.9216 0.9216 0.9216 AUTHOR ::::EMDATABANK.org::::EMD-15973::::