Structure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana

2026-08-12 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp_atom.pdbx_stereo_config _em_admin.last_update PDBj PDBc 2023-03-30 2023-10-25 2023-10-25 2026-08-12 Chinese Academy of Sciences 2019YFA0906300 China Chinese Academy of Sciences 2021YFA1300403 China Chinese Academy of Sciences XDA26050402 China Chinese Academy of Sciences XDB17000000 China Chinese Academy of Sciences 2020081 China Chinese Academy of Sciences JCTD-2020-06 China Chinese Academy of Sciences YSBR-004 China Chinese Academy of Sciences 31970260 China Chinese Academy of Sciences 32222007 China Structure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana Feng Y Li ZH Wang WD Shen JR PSII supercomplex, LHCX, FCP, PHOTOSYNTHESIS Feng Y Li Z Li X Shen L Liu X Zhou C Zhang J Sang M Han G Yang W Kuang T Wang W Shen JR Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII. Sci Adv US 9 eadi8446 eadi8446 2023 37878698 doi:10.1126/sciadv.adi8446 2375-2548 8iwh FULLOVERLAP EMDB EMD-35766 associated EM volume

Structure of PSII-FCPII supercomplex containing monomeric LHCX and dimeric FCPII from Thalassiosira pseudonana Structure of PSII-FCPII supercomplex containing monomeric LHCX and dimeric FCPII from Thalassiosira pseudonana 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 Thalassiosira pseudonana Photosystem II protein D1 Thalassiosira pseudonana 0.036982176 2 LEVO VSLWERFCAWITSTENRLYIGWFGCLMFPTLLTATSCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISGAVIPSSNAIG MHFYPIWEAASVDEWLYNGGPYQLIVLHFLLGVASYMGREWELSYRLGMRPWIFVAFSAPVAAASAVFLVYPIGQGSFSD GMPLGISGTFNFMLVFQAEHNILMHPFHMAGVAGVFGGSLFSAMHGSLVTSSLIRETTENESTNYGYKFGQEEETYNIVA AHGYFGRLIFQYASFNNSRALHFFLALWPVLGIWLTAMGISTMAFNLNGFNFNQSVVDSQGRVINTWADIINRADLGMEV MHERNAHNFPLDL A0T0W2 1.10.3.9 Photosystem II CP47 reaction center protein Thalassiosira pseudonana 0.056465262 2 LEVO MALPWYRVHTVVLNDPGRLISVHLMHTALVAGWAGSMALYELAVFDPSDPVLNPMWRQGMFVMPFMTRLGITDSWGGWSI TGESVSNPGLWSFEGVALSHIVLSGMCFLAAIWHWVYWDLELFRDPRTGEPALDLPKIFGIHLLLSGLLCFGFGAFHVTG LFGPGIWVSDAYGITGKVQPVAPSWGADGFNPFNPGGIAAHHIAAGIFGIFAGIFHLTVRPPQRLYRALRMGNIETVLSS SISAVFWAAFVTSGTMWYGAAATPIELFGPTRYQWDSGYFQQEIERQVESSVTEGLSESQAWSRIPDKLAFYDYIGNNPA KGGLFRSGPMDKGDGIAEAWLGHPIFRDKDGRELTVRRMPAFFETFPVILVDKDGIIRADIPFRRAESKYSIEQVGVTVD FYGGKLNGQTFKDAPTVKKFARKAQLGEVFEFDRTSLESDGVFRSSPRGWYTFGHANFALLFFLGHLWHGGRTIFRDVFT GIGAEVTEQVEFGAFQKLGDKTTKKQGAV A0T0P5 Photosystem II CP43 reaction center protein Thalassiosira pseudonana 0.051776156000000004 2 LEVO MKTLYSLRRYYHVETPFNSSIAGRDIESTGFAWWSGNARLINVSGKLLGAHVAHAGLMVFWAGAMILFEVSHFVPEKPLY EQGFICMQHLATLGYGIGPGGEITSTVPYFAVGVIHLISSAVLGFGGIYHSLLGPDTLEESFPFFGYDWRDKNKMTTILG IHLCLLGLGALLLVAKAMYLGGVYDTWAPGGGDVRYITTPTLNPIVIFGYVFRSPFGGDGWVVSVNNMEDLVGGHIWVGI LCIVGGVWHIFTKPFSWARRAFVWSGEAYLSYSLAAISLMGFTASLYAWYNNTAYPSELYGPTGPEASQSQAFTFLVRDQ RLGANVSSAQGPTGLGKYLMRSPSGEIIFGGETMRFWDLRAPWVEPLRGPNGLDINKIKNDIQPWQERRAAEYMTHAPLG SLNSVGGVATEINSVNYVSPRSWLCCSHFFLGFFFLIGHWWHSGRARAAAAGFEKGINRANEPVLSMRPI A0T0T1 Photosystem II D2 protein Thalassiosira pseudonana 0.039089582 2 LEVO MTIAIGQNQERGLFDLVDDWLKRDRFVFVGWSGILLFPTAYLAAGGWFTGTTFVTSWYTHGLASSYLEGCNFLTAAVSTP ANSMGHSLLLLWGPEAQGDFTRWCQIGGLWAFIALHGAFGLIGFCLRQFEIARLVGIRPYNAIAFSGPIAVFVSVFLLYP LGQASWFFAPSFGVAAIFRFLLFLQGFHNWTLNPFHMMGVAGILGGALLCAIHGATVENTLFEDGDAANTFRAFTPTQSE ETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPVAGLWTSSIGIVGLALNLRAYDFVSQELRAAEDPEFETFYTKNILL NEGIRSWMAAQDQPHENFVFPEEVLPRGNAL A0T0T0 1.10.3.9 Cytochrome b559 subunit alpha Thalassiosira pseudonana 0.009521691999999998 2 LEVO MSGGSTGERPFSDIITSVRYWIIHTITIPSLFVSGWLFISTGLAYDVFGTPRPNEYFTQDRQQVPLVNDRFSAKQELEDL TKGL A0T0U2 Cytochrome b559 subunit beta Thalassiosira pseudonana 0.0049138459999999995 2 LEVO MTKNINQPVAYPIFTFRWLAVHGLAIPTVFFLGGITAMQFIQR A0T0U1 Photosystem II Psb31 protein domain-containing protein Thalassiosira pseudonana 0.018176705 2 LEVO MKIIALCLVASAAAFAPAPVERASTSLNMDRRMATAQIATSAAVLAGLPSLALADGAKSAATQSRARGIYGQRIAALESA VNAGDFGAVAAEKNAFILFNSGAIADKSKKSEAVKQTNAIFAAIRAKDAGALKSAYATYKGANDIKVIVADKESGQGYSN DYDFKARTTLGTIYVR B8CC14 Photosystem II reaction center protein H Thalassiosira pseudonana 0.007391801 2 LEVO MALRTRLGEILRPLNAEYGKVVPGWGTTPIMGLTMVLFLVFLLIILQIYNSSLIIENVDVDWANAI A0T0P8 Photosystem II reaction center protein I Thalassiosira pseudonana 0.003940673 2 LEVO MLTLKILVYTTVIFFVSLFIFGFLSSDPSRNPNR A0T0U9 Photosystem II reaction center protein J Thalassiosira pseudonana 0.004045768 2 LEVO MVNTGRVPLWLVGLVGGFAVITIVSLFIYGSYSGLGSSL A0T0T9 Photosystem II reaction center protein K Thalassiosira pseudonana 0.00498399 2 LEVO MESLLLARLPEAYVVFSPLVDVFPVIPVFFLLLAFVWQAAVGFR A0T0S8 Photosystem II reaction center protein L Thalassiosira pseudonana 0.004367076 2 LEVO MTGPNPNKQAVELNRTSLYWGLLLIFVLAVLFSSYFFN A0T0U0 Photosystem II reaction center M protein, plastid Thalassiosira pseudonana 0.012051049999999999 2 LEVO MKSFQIVTLFAMIAATMAFAPNKAPQVAQRFAESGFDMKKAAIAAIPAAIATPAFAMDSIVEALPTQTLSLEVQFGAYLA VLLGTFLPVLFLINLYIQTESRKAGRDGGIDSE B8BYH2 Photosystem II subunit, PsbN. Thalassiosira pseudonana 0.0025711609999999998

Author stated that sequence was not found

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)(UNK)(UNK)(UNK)(UNK)(UNK) Oxygen-evolving enhancer protein 1 Thalassiosira pseudonana 0.032168496 2 LEVO MKLVAALSLVAGVSAFAPAQTNSRSTQLNAMKDDIAKVGAAALASAAIFGITAAPAQAITKSELNQLSYLQVKGTGLANR CSEVIGEDTITPKSGARLVDMCIEPKAWAVEEEIGKAGKTEKKFVNSKVMTRQTYTLEGIEGSLKTDGGKIVFTEEEGID YAPTTVQLPGGERVPFLFTVKELVATGNGGAFKPGFQMGGDFSVPSYRTGLFLDPKGRGGVTGYDMAVALPGLQSGEEGD AELFKENNKTFEVGNGRIEMEVNKVNAEESEIGGVFVASQSGDTDMGSKVPKKILTKGIFYAKIQ B8C4I5 Photosystem II reaction center protein T Thalassiosira pseudonana 0.003314011 2 LEVO MEALVYTFLLIGTLMVIFFAVFFRDTPR A0T0P6 PS II complex 12 kDa extrinsic protein Thalassiosira pseudonana 0.015486595999999998 2 LEVO MKLAVIAALVSSAAAFAPNAQPAAQTALNAESDRRSFLGAAAAFGAAALPLAANAVVDYENVALLGGSQTVDLNNANVRA YLRMPGMYPAAAGKIVTHGPYKSVADVYNIPGLTNAEKEVIKKYESRFTAKAVAPEYAIDRINNGLYR B8BVI4 Cytochrome c-550 Thalassiosira pseudonana 0.017713232 2 LEVO MFKTYSKSFACILFCIFNIFVVSASAIDLDEATRTVVTDSSGNTTVLTPEQVKRGKRLFNATCGACHTGGITKTNPNVGL DPEALSLATPRRDNISALVDYLKNPTTYDGLESIAEIHPSIKSADIYPRMRSLTDEDLYSIAGHIMLQPKIVAEKWGGGK IY A0T0N2 Photosystem II subunit, PsbW Thalassiosira pseudonana 0.006096549 2 LEVO TEGTNEWFGVDDIRVLAVLFIGHYFILSLWLGQYGNATEDDDADFFGEIDYTGS B8C8Y3 Photosystem II reaction center X protein Thalassiosira pseudonana 0.003933643 2 LEVO MTTSLANFIASLTAGALVLSAIGIALIIISKNDRVQRS A0T0N4 Photosystem II reaction center protein Z Thalassiosira pseudonana 0.006417546 2 LEVO MITALTALFVLVSLALVVTVPVALATPGEWETSKDQFNKIFQLWVGLVVAIATADGISTAI A0T0T3 Fucoxanthin chl a/c protein, lhca clade Thalassiosira pseudonana 0.02410099 1 LEVO WNEAPRALPFGSAPPTLDGSLVGDVGFDPIGFSTAPFASFNNPIYQEGNFMTDVQWLREAELTHGRIAQLAVVGFIWPAL FGTFPGNENFGGADAYSYVNPLEAINHIPSLAIYQIVGGMAWVEYQRVQRIKEQGKDRISGDIGLAYPGGWNPFNINYSP EEYAEKQLQEIKHCRLAMLGAFGLFFQALNSGEDIVSQLSPAFAAPEYAAKAGYFLPQGI B8BUU4 Fucoxanthin-chlorophyll a-c binding protein, plastid Thalassiosira pseudonana 0.021058960999999998 1 LEVO MMKLAVFASLIAGSSAFAPAQVGRASTSVQAFENEIGVLPPTGFFDPAGLSDGISQEKFDSYRLAELKHGRAAMLAVLGY VAPETYRFGYDLIPGELSTNDIPNGVAAIKAIPFGGWAQMIAFVGCVETYGWFTSPTGVLDLPDDILAKRQTAELQHGRL AMLAFLELIRHDSQNLAQPGFDGLDNLITGLPFLYN B8BVI1 Fucoxanthin chlorophyll a/c protein 6 Thalassiosira pseudonana 0.020872669999999996 1 LEVO MYKSLLIASSIAAASAFAPVQVAKTTTSLNAFESEIGAQAPLGFWDPLGFLDRADQETFDRLRYVELKHGRIAQLAFVGN LITRAGYHLPGDISLGRAFADVPNGIAAINGPDAISTAALLQTLAFIGFLETRVMIDATGESQFRGDFRNGFDFGWDKQS PEWQTNKRAIELNQGRAAMMGILGLMMHEQVG B8BX92 Fucoxanthin chlorophyll a/c protein 5 Thalassiosira pseudonana 0.021402484 1 LEVO MYKSLLIASSIAAASAFAPAPVAKSTTAINAFENELGAQPPLGFFDPLGMLDEAGQARFDRLRYVELKHGRICQLAFLGN IITRAGIHLPGAISLDGTKFSDIGNGWAGSFEVPKDGALQILFFVGFLELFVMKDVTGEGEFVGDFRNGALDFGWDSFSE ETKLQKRAIELNNGRAAMMGILGLMVHEQLGGELPIVGQ B8CEV5 Fucoxanthin chlorophyll a/c protein-LI818 clade Thalassiosira pseudonana 0.021279365 2 LEVO MKLAIISTLIAGAAAFAPQTVGPSTSALSATRAGLVGALPPVGFFDPAGFAAKASPEELARYREVEIMHGRFAQMAVLGF IIPEKCAYDGAFGDDFLAPTGRALEAINTDPVWLALTLGVISALETLRLLQTEPGTRTDAKIEGLGWRPKSEAEFVNYQV RELQQGRLAMLAFAGEIAQELVNEKPLLVNLQDSGFVSW B5YLU3 Photosystem II reaction center protein Ycf12 Thalassiosira pseudonana 0.003591463 2 LEVO MVNWQVIGQLVSTGAIMLLGPAIIILLALKKGNL A0T0T2 Photosystem II subunit, PsbQ. Thalassiosira pseudonana 0.022439217 2 LEVO MKIVLALVAASSVSAFAPQSNGRQSVAMQAENSRREALSTIAAATAAILPAAANAAAGESPRFSVFGVIGDGTSYSEGAA YGSDQSAETYSPYSVYGKVGSKDALFEAGNAGEIARKKGYIVESQKRLKNLPGYVEKKQWFNVKDELTRYMYETRGAVRG LAQTPEQKKLAKAFFQAIEEASLQATLKNGDKCAAASADSIKLLDQFYASL B8BSY9 Fucoxanthin chlorophyll a/c light-harvesting protein, major type Thalassiosira pseudonana 0.020786684 4 LEVO MKSVIIASLACSAAAFAPAQVGRSSTAVQGFENEPGVIAPTGFFDPLGFTDDIDQEKFDQYRTAELKHGRVAQLAVIGYI VPEIFRWGFDIAPGVACADVPNGVAAIDAIPALGWAQIIFAIGAVDVRGWFGNFDIGKPDLKGKDEERALQELQHGRLAM LAILELLRHDSQNLVKPGFDGLDNLITGLPFLY B8BX93 BETA-CAROTENE 0.000536873 22 BCR CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX CHLORIDE ION 3.5453e-05 2 CL CHLOROPHYLL A 0.000893489 183 CLA PHEOPHYTIN A 0.0008712 4 PHO BICARBONATE ION 6.1017e-05 2 BCT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 20 LHG 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 12 SQD DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 11 DGD 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 26 LMG FE (II) ION 5.5845e-05 2 FE2 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 2 PL9 PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM DODECYL-ALPHA-D-MALTOSIDE 0.000510615 6 LMU Chlorophyll c1 0.000610941 3 KC1 (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate 0.0006589059999999999 29 A86 (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol 0.000582855 10 DD6 Chlorophyll c2 0.000608926 5 KC2 (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol 0.000566856 2 ET4 singleParticle particle 6.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.68 FSC 0.143 CUT-OFF 97098 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_35766.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.24096127 0.7193644 0.0009805791 0.023143515 0.88 0.88 0.88 0.088 AUTHOR ::::EMDATABANK.org::::EMD-35766:::: emd_35766_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.57627535 0.97734743 0.0012359692 0.08334765 0.88 0.88 0.88 AUTHOR ::::EMDATABANK.org::::EMD-35766:::: emd_35766_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.5873387 0.99347353 0.0012154989 0.08345815 0.88 0.88 0.88 AUTHOR ::::EMDATABANK.org::::EMD-35766::::