Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted)

2025-07-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY atom_site chem_comp_atom chem_comp_bond database_PDB_caveat em_admin em_entity_assembly_molwt em_software entity entity_name_com entity_src_nat pdbx_entry_details pdbx_modification_feature pdbx_struct_conn_angle pdbx_unobs_or_zero_occ_atoms pdbx_validate_chiral pdbx_validate_close_contact struct_conn struct_conn_type _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _atom_site.type_symbol _em_admin.last_update _em_entity_assembly_molwt.id _em_software.name _entity.pdbx_description _entity_src_nat.common_name _pdbx_entry_details.has_protein_modification STRUCTURE_SUMMARY em_admin em_entity_assembly_molwt em_software entity entity_src_nat _em_admin.last_update _em_entity_assembly_molwt.id _em_software.name _entity.pdbx_description _entity_src_nat.common_name PDBe PDBe 2021-06-11 2021-08-18 2021-08-18 2025-07-02 Swedish Research Council 2016-05009 Sweden Other private Carl Trygger Sweden Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted) Graca AT Hall M Oxidoreductase, Complex, PHOTOSYNTHESIS Graca AT Hall M Persson K Schroder WP High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Sci Rep UK 11 15534 15534 2021 34330992 doi:10.1038/s41598-021-94914-x 2045-2322 Afonine PV Poon BK Read RJ Sobolev OV Terwilliger TC Urzhumtsev A Adams PD Real-space refinement in PHENIX for cryo-EM and crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. DK 74 531 544 2018 0907-4449 0766 ABCRE6 7oui FULLOVERLAP Photosystem II - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type) Photosystem II - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Arabidopsis thaliana Wildtype Leaf Chloroplast Thylakoid Membrane CP24-LHCII (M-trimer) 1 1 2 3 Arabidopsis thaliana Wildtype Leaf Chloroplast Thylakoid Membrane LHCII S-trimer 1 21 22 23 Arabidopsis thaliana Wildtype Leaf Chloroplast Thylakoid Membrane CP29 1 22 Arabidopsis thaliana Wildtype Leaf Chloroplast Thylakoid Membrane CP26 1 20 Arabidopsis thaliana Wildtype Leaf Chloroplast Thylakoid Membrane Photosystem II core complex (dimer) 1 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 Arabidopsis thaliana Wildtype Leaf Chloroplast Thylakoid Membrane Chlorophyll a-b binding protein, chloroplastic Arabidopsis thaliana 0.028193934 4 LEVO MAASTMALSSPALTGKAVKLSPAASEVFGTGRITMRKASKPTGPSGSPWYGSDRVKYLGPFSGEPPSYLTGEFPGDYGWD TAGLSADPETFARNRELEVIHSRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSDGGLDYLGNPSLVHAQSILAI WATQVILMGAVEGYRVAGDGPLGEAEDLLYPGGSFDPLGLATDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPL ENLADHLADPVNNNAWAFATNFVPGK Q39142 Chlorophyll a-b binding protein 3, chloroplastic Arabidopsis thaliana 0.02645299 2 LEVO ASSFNPLRDVVSLGSPKYTMGNDLWYGPDRVKYLGPFSVQTPSYLTGEFPGDYGWDTAGLSADPEAFAKNRALEVIHGRW AMLGAFGCITPEVLQKWVRVDFKEPVWFKAGSQIFSEGGLDYLGNPNLVHAQSILAVLGFQVILMGLVEGFRINGLDGVG EGNDLYPGGQYFDPLGLADDPVTFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLLDHLDNPVANNAWAFATKFA PGA Q9S7M0 Chlorophyll a-b binding protein, chloroplastic Arabidopsis thaliana 0.023198286999999998 2 LEVO AAAAAQPKKSWIPAVKGGGNFLDPEWLDGSLPGDFGFDPLGLGKDPAFLKWYREAELIHGRWAMAAVLGIFVGQAWSGVA WFEAGAQPDAIAPFSFGSLLGTQLLLMGWVESKRWVDFFNPDSQSVEWATPWSKTAENFANYTGDQGYPGGRFFDPLGLA GKNRDGVYEPDFEKLERLKLAEIKHSRLAMVAMLIFYFEAGQGKTPLGALGL Q9LMQ2 Photosystem II protein D1 Arabidopsis thaliana 0.038830082 2 LEVO TAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGA IIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIY PIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQ EEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGFNFNQSVVDSQGRVINTWADII NRANLGMEVMHERNAHNFPLDLAAVEAPSTNG P83755 1.10.3.9 Photosystem II CP47 reaction center protein Arabidopsis thaliana 0.056091824 2 LEVO MGLPWYRVHTVVLNDPGRLLAVHIMHTALVAGWAGSMALYELAVFDPSDPVLDPMWRQGMFVIPFMTRLGITNSWGGWNI TGGTITNPGLWSYEGVAGAHIVFSGLCFLAAIWHWVYWDLEIFCDERTGKPSLDLPKIFGIHLFLSGVACFGFGAFHVTG LYGPGIWVSDPYGLTGKVQPVNPAWGVEGFDPFVPGGIASHHIAAGTLGILAGLFHLSVRPPQRLYKGLRMGNIETVLSS SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDQGYFQQEIYRRVSAGLAENQSLSEAWAKIPEKLAFYDYIGNNPA KGGLFRAGSMDNGDGIAVGWLGHPVFRNKEGRELFVRRMPTFFETFPVVLVDGDGIVRADVPFRRAESKYSVEQVGVTVE FYGGELNGVSYSDPATVKKYARRAQLGEIFELDRATLKSDGVFRSSPRGWFTFGHASFALLFFFGHIWHGARTLFRDVFA GIDPDLDAQVEFGAFQKLGDPTTKRQAV P56777 Photosystem II CP43 reaction center protein Arabidopsis thaliana 0.050086324 2 LEVO TLFNGTLALAGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVAHFVPEKPMYEQGLILLPHLAT LGWGVGPGGEVIDTFPYFVSGVLHLISSAVLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTILGIHLILLGVGAFL LVFKALYFGGVYDTWAPGGGDVRKITNLTLSPSVIFGYLLKSPFGGEGWIVSVDDLEDIIGGHVWLGSICIFGGIWHILT KPFAWARRALVWSGEAYLSYSLAALSVCGFIACCFVWFNNTAYPSEFYGPTGPEASQAQAFTFLVRDQRLGANVGSAQGP TGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGVATEI NAVNYVSPRSWLSTSHFVLGFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN P56778 Photosystem II D2 protein Arabidopsis thaliana 0.039444082 2 LEVO TIALGKFTKDEKDLFDIMDDWLRRDRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGLASSYLEGCNFLTAAVST PANSLAHSLLLLWGPEAQGDFTRWCQLGGLWAFVALHGAFALIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIY PLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQA EETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSALGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNIL LNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL P56761 1.10.3.9 Cytochrome b559 subunit alpha Arabidopsis thaliana 0.009393501 2 LEVO MSGSTGERSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITGRFDSLEQLDEFS RSF P56779 Cytochrome b559 subunit beta (PsbF) Arabidopsis thaliana 0.004428228 2 LEVO MTIDRTYPIFTVRWLAVHGLAVPTVSFLGSISAMQFIQR P62095 Photosystem II reaction center protein H Arabidopsis thaliana 0.007575691 2 LEVO ATQTVEDSSRSGPRSTTVGKLLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIILEIYNSSVLLDGISVN P56780 Photosystem II reaction center protein I Arabidopsis thaliana 0.0041708909999999995 2 LEVO MLTLKLFVYTVVIFFVSLFIFGFLSNDPGRNPGREE P62100 Photosystem II reaction center protein K Arabidopsis thaliana 0.004239112 2 LEVO KLPEAYAFLNPIVDVMPVIPLFFLLLAFVWQAAVSFR P56782 Photosystem II reaction center protein L Arabidopsis thaliana 0.004471075 2 LEVO MTQSNPNEQSVELNRTSLYWGLLLIFVLAVLFSNYFFN P60129 Photosystem II reaction center protein M Arabidopsis thaliana 0.003783538 2 LEVO MEVNILAFIATALFILVPTAFLLIIYVKTVSQND P62109 Oxygen-evolving enhancer protein 1-1, chloroplastic Arabidopsis thaliana 0.026594638999999996 2 LEVO EGAPKRLTYDEIQSKTYMEVKGTGTANQCPTIDGGSETFSFKPGKYAGKKFCFEPTSFTVKADSVSKNAPPEFQNTKLMT RLTYTLDEIEGPFEVASDGSVNFKEEDGIDYAAVTVQLPGGERVPFLFTVKQLDASGKPDSFTGKFLVPSYRGSSFLDPK GRGGSTGYDNAVALPAGGRGDEEELVKENVKNTAASVGEITLKVTKSKPETGEVIGVFESLQPSDTDLGAKVPKDVKIQG VWYGQLE P23321 Photosystem II reaction center protein T Arabidopsis thaliana 0.0038256419999999998 2 LEVO MEALVYTFLLVSTLGIIFFAIFFREPPKISTKK P61839 Photosystem II reaction center W protein, chloroplastic Arabidopsis thaliana 0.006036748999999999 2 LEVO LVDERMSTEGTGLPFGLSNNLLGWILFGVFGLIWTFFFVYTSSLEEDEESGLSL Q39194 (thale cress) hypothetical protein Arabidopsis thaliana 0.004186916 2 LEVO AGSGISPSLKNFLLSIASGGLVLTVIIGVVVGVSNFDPVKRT A0A7G2E9B1 Photosystem II reaction center protein Z Arabidopsis thaliana 0.006569768 2 LEVO MTIAFQLAVFALIITSSILLISVPVVFASPDGWSSNKNVVFSGTSLWIGLVFLVGILNSLIS P56790 Chlorophyll a-b binding protein CP26, chloroplastic Arabidopsis thaliana 0.025232754 2 LEVO SKAVSETSDELAKWYGPDRRIFLPDGLLDRSEIPEYLNGEVAGDYGYDPFGLGKKPENFAKYQAFELIHARWAMLGAAGF IIPEALNKYGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVLAVVAEVVLLGGAEYYRITNGLDFEDKLHPGGPFDP LGLAKDPEQGALLKVKEIKNGRLAMFAMLGFFIQAYVTGEGPVENLAKHLSDPFGNNLLTVIAGTAERAPTL Q9XF89 Chlorophyll a-b binding protein 1, chloroplastic Arabidopsis thaliana 0.024885071999999998 6 LEVO RKTVAKPKGPSGSPWYGSDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFARNRELEVIHSRWAMLGALGCVF PELLARNGVKFGEAVWFKAGSQIFSDGGLDYLGNPSLVHAQSILAIWATQVILMGAVEGYRVAGNGPLGEAEDLLYPGGS FDPLGLATDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPIENLADHLADPVNNNAWAFATNFVPGK P04778 Chlorophyll a-b binding protein CP29.1, chloroplastic Arabidopsis thaliana 0.027302854999999997 2 LEVO AAPKKSAKKTVTTDRPLWYPGAISPDWLDGSLVGDYGFDPFGLGKPAEYLQFDIDSLDQNLAKNLAGDVIGTRTEAADAK STPFQPYSEVFGIQRFRECELIHGRWAMLATLGALSVEWLTGVTWQDAGKVELVDGSSYLGQPLPFSISTLIWIEVLVIG YIEFQRNAELDSEKRLYPGGKFFDPLGLAADPEKTAQLQLAEIKHARLAMVAFLGFAVQAAATGKGPLNNWATHLSDPLH TTIIDTFSSS Q07473 Photosystem II 5 kDa protein, chloroplastic Arabidopsis thaliana 0.00317881 2 LEVO EPKRGTEAAKKKYAQVCVTMPTAKICRY Q39195 CHLOROPHYLL B 0.000907472 60 CHL CHLOROPHYLL A 0.000893489 162 CLA 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 30 LHG PHEOPHYTIN A 0.0008712 4 PHO BETA-CAROTENE 0.000536873 22 BCR 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 8 SQD 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 12 LMG 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 Digitonin 0.0012293119999999998 22 AJP BICARBONATE ION 6.1017e-05 2 BCT FE (II) ION 5.5845e-05 2 FE2 DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 8 DGD CALCIUM ION 4.0078e-05 4 CA CHLORIDE ION 3.5453e-05 2 CL PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 18 LUT (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 10 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 2 XAT water 1.8015e-05 139 HOH singleParticle particle 1 7.5 HEPES-KOH

10mM HEPES-KOH pH7.5 + 0.01% (w/v) digitonin

Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE 30

50 mA

ETHANE 100 277.15 FEI VITROBOT MARK IV

Blot force -5 Wait time 1s Blotting time 5s.

Indicated sample concentration based on Chlorophyll measurement.

FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 12227 1.49 1 cryoSPARC 2.15 NONE 5MDX 2.79 FSC 0.143 CUT-OFF cryoSPARC 2.15 100712 ANGULAR RECONSTITUTION cryoSPARC 2.15 ANGULAR RECONSTITUTION cryoSPARC 2.15 emd_13078.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 410.0 410.0 410.0 90.0 90.0 90.0 Z Y X -19.496286000000001 33.681809999999999 -0.0038570869 0.9759321 0.82 0.82 0.82 4.0 AUTHOR ::::EMDATABANK.org::::EMD-13078::::