2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Ligand identity

Changed water molecules as requested by reviewer

STRUCTURE_SUMMARY atom_site chem_comp database_PDB_caveat em_imaging em_software entity pdbx_contact_author pdbx_distant_solvent_atoms pdbx_entity_nonpoly pdbx_initial_refinement_model pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_validate_chiral pdbx_validate_close_contact pdbx_validate_polymer_linkage pdbx_validate_rmsd_angle pdbx_validate_torsion refine_ls_restr software struct_asym struct_conf struct_conn struct_mon_prot_cis struct_sheet struct_sheet_order struct_sheet_range _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type _em_imaging.nominal_cs _em_imaging.nominal_defocus_max _em_imaging.nominal_defocus_min _pdbx_struct_assembly_gen.asym_id_list _refine_ls_restr.dev_ideal _refine_ls_restr.number _software.version _struct_mon_prot_cis.pdbx_omega_angle DATABASE_REFERENCES citation citation_author _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name COORDINATE_REPLACEMENT AUTHOR Atomic clashes STRUCTURE_SUMMARY atom_site chem_comp_atom chem_comp_bond database_PDB_caveat em_3d_fitting_list em_admin em_software entity entity_name_com pdbx_distant_solvent_atoms pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_assembly pdbx_struct_assembly_gen pdbx_struct_conn_angle pdbx_struct_oper_list pdbx_unobs_or_zero_occ_atoms pdbx_validate_chiral pdbx_validate_close_contact pdbx_validate_main_chain_plane pdbx_validate_polymer_linkage pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond refine refine_ls_restr software struct_asym struct_conn struct_ref struct_ref_seq struct_ref_seq_dif _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _entity.formula_weight _entity.pdbx_description _entity.pdbx_number_of_molecules _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_struct_assembly.details _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_oper_list.symmetry_operation _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.details _pdbx_validate_close_contact.auth_seq_id_2 _refine.ls_d_res_high _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_accession STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp.formula _chem_comp_atom.pdbx_stereo_config _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2021-08-19 2022-08-17 2022-08-17 2026-09-16 Israel Science Foundation 569/17 Israel Israel Science Foundation 199/21 Israel Caspy I Fadeeva M green algae, photosystem II, thylakoid, oxygen evolving complex, cryo-EM, stacking, PHOTOSYNTHESIS Caspy I Fadeeva M Mazor Y Nelson N Elife US 12 2023 36799903 doi:10.7554/eLife.81150 2050-084X 7pi0 FULLOVERLAP EMDB EMD-13429 associated EM volume

Unstacked compact Dunaliella PSII

Dunaliella salina Photosystem II complex Dunaliella salina Photosystem II complex 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 Dunaliella salina Photosystem II protein D1 Dunaliella salina 0.037291488 2 LEVO ENTSLWARFCEWITSTENRLYIGWFGVIMIPTLLTAISVYIIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPTSNA IGLHFYPIWEAASLDEWLYNGGPYQLVVCHFFLGVCCYMGREWELSYRLGMRPWIAVAYSAPVAAATAVFIIYPIGQGSF SDGMPLGISGTFNFMIVFQAEHNILMHPFHMFGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANAGYKFGQEEETYNI VAAHGYFGRLIFQYASFNNSRSLHFFLAVWPVVCIWLTALGISTMAFNLNGFNFNQSVVDSNGRVLNTWADIINRANLGM EVMHERNAHNFPLDLA D0FY08 1.10.3.9 Photosystem II CP47 reaction center protein Dunaliella salina 0.053321516 2 LEVO GLPWYRVHTVVINDPGRLISVHLMHTALVAGWAGAMTLFEIAVFDPSDPVLNPMWRQGMFVLPFLTRLGVTQSWGGWTIS GETSSNPGIWSYEGAAASHIVLSGLLFLASVWHWVYWDLELFRDPRTGKTALDLPKIFGIHLFLAGLLCFGFGAFHVTGV FGPGIWVSDPYGLTGSVQPVAPSWGAEGFDPYNPGGVPAHHIAAGILGVLAGLFHL(CSD)VRPSIRLYFGLSMGSIESV LSSSIAAVFWAAFVVAGTMWYGSAATPIELFGPTRYQWDQGFFQQEIQKRVAQSTSEGLSVSEAWAKIPEKLAFYDYIGN NPAKGGLFRTGAMNSGDGIAVGWLGHASFKDQEGRELFVRRMPTFFETFPVVLIDKDGVVRADVPFRKAESKYSIEQVGV SVTFYGGELNGLTFTDPSTVKKYARKAQLGEIFEFDRSTLQSDGVFRSSPRGWFTFGHLSFALLFFFGHIWHGSRTIFRD VFAGIDED A0A1C8XRM6 Photosystem II reaction center protein Ycf12 Dunaliella salina 0.003217949 2 LEVO SLTLILQLVALFAVVAAGPLVVVLLSVRGGNL D0FY13 Photosystem II CP43 reaction center protein Dunaliella salina 0.049128991999999996 2 LEVO GRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVSHFVPEKPMYEQGLILLPHIATLGYGVGPGGE VLDTFPYFVSGVLHLISSAVLGFGGVYHSLIGPETLEESYPFFGYVWKDKNKMTNILGYHLIILGCGAWLLVLKALYFGG VYDTWAPGGGDVRIISNPTTNAAIIFGYIVKSPFGGDGWIVSVDNLEDIIGGHIWIGTLCILGGIWHIYTTPWPWARRAF VWSGEAYLSYSLAAVSLMGFTACCFAWFNNTAYPSEFYGPTGPEASQAQAFTFLVRDQRLGANVASAQGPTGLGKYLMRS PTGEIIFGGETMRFWDFRGPWVEPLRGPSGLDLVKLKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINAVNFVSPRS WLATSHFCLGFFFFVGHLWHAGRARAAAAGFEKGIDRVDEPVLSMRPLD D0FXY3 Photosystem II D2 protein Dunaliella salina 0.038965383 2 LEVO IGTYQEKRTWFDDADDWLRQDRFVFVGWSGLLLLPCAYFAVGGWLTGCTFVTSWYTHGLASSYIEGCNFLTAAVSTPANS LGHSLLFVWGPEAQGDLTRWFQLGGLWAFVALHGAFGLIGFMLRQFEIARSVNLRPYNAIAFSAPIAVFVSVFLIYPLGQ SGWFFAPSFGVASIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQAEETY SMVTANRFWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSALGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNILLNEG IRAWMAAQDQPHEKLTLPEEVLPRGNAL A0A1C8XRK9 1.10.3.9 Cytochrome b559 subunit alpha Dunaliella salina 0.008743846999999999 2 LEVO ERPFSDILTSIRYWVIHSITVPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTEDRQDAPLITDRFNALEQVKKLSAQ D0FY01 Cytochrome b559 subunit beta Dunaliella salina 0.0035492989999999997 2 LEVO IFTVRWLAIHAIAVPTIFFLGAITAMQFIQR A0A1C8XRP4 Photosystem II reaction center protein H Dunaliella salina 0.007124381 2 LEVO EPGIVTPLGTLLRPLNSEAGKVLPGWGTTVLMAVAILLFAVFLLIILEIYNSSLILDGVTNSWESLA A0A1C8XRP3 Photosystem II reaction center protein I Dunaliella salina 0.003929648 2 LEVO MLTLKIFVYTVVTFFVGLFIFGFLSNDPSRNPGKG D0FXX5 Photosystem II reaction center protein J Dunaliella salina 0.0037375 2 LEVO IGRIPLWLVGTVVGLLAIGLLAIFFYGSYVGLGSSL Photosystem II reaction center protein K Dunaliella salina 0.004159991 2 LEVO KLPEAYAPFSPIVDVLPIIPVLFILLAFVWQASVSFR D0FXX2 Photosystem II reaction center protein L Dunaliella salina 0.004417203000000001 2 LEVO MARPNPNKQVVELNRSSLYWGLLLIFVLAVLFSSYIFN D0FY19 Photosystem II reaction center protein M Dunaliella salina 0.0033079789999999995 2 LEVO VNILGLTATALFIIIPTSFLLILYVKTAASE Oxygen-evolving enhancer protein 1, chloroplastic Dunaliella salina 0.025874908 2 LEVO LTYDELQGLTYLQVKGTGIANTCPVVEQGTSNVRELKPGDYKLEKFCMEPTSFTVKEEDAKGREEFVKTKLLTRLTYGLD GMNGSMKINNDGSVEFREDEGLDYAATTVKLPGGEYVPFLFTIKEFDGKGTLDSFSGDFLVPSYRGSTFLDPKGRGGATG YDNAIALPAKADADEIQRLNNKSYTPGKGSAVFSVAKVDTETGEIAGVFESIQPSDTEMGAHPAKDIKITGLWYGQLT Oxygen-evolving enhancer protein 2, chloroplastic Dunaliella salina 0.020425706999999998 2 LEVO AYGEGANVFGRVTNKSGFVPYAGDSFALLLPSKWNPSDEKEVDSIVLRYADNFDAVNNVYVIAQDTDKSSIQDYGSPEEF ISQFGYLLGRQAWAGQTVSEGGFDANKVSSAALLGVATEKDKKGKTYYKFEILSRTADGNEGGRHQLVKATVSNGKLYLL KVQAGDKRWFKGTDKECLGVLDSFTVV Photosystem II reaction center protein T Dunaliella salina 0.003478194 2 LEVO MEALVYTFLLIGTLGIIFFSIFFREPPRIA D0FY04 PSII 6.1 kDa protein Dunaliella salina 0.004698315 2 LEVO LVDDRMNGDGTGLPFGVNDGILGWVIAGTLGTIWAIYFVSQKDL Hypothetical protein Dunaliella salina 0.002854407 2 LEVO SVTPSLKNFLLSLVAGAVVLAAIAGAVTAV Photosystem II reaction center protein Z Dunaliella salina 0.006430616 2 LEVO MTSILQIALLGLVLVSFALVVGVPVVFASPNGWTENKGVVFSGLSVWFLLVFAVGVFNSFA D0FXZ2 Chlorophyll a-b binding protein of LHCII type 3, chloroplastic Dunaliella salina 0.024075081999999998 2 LEVO TINQFYGPDRNKWLGPYSTNTPPYLTGEFPGDYGWDTAGLSADPETFKRYRELELIHARWALLGALGMVTPELLQDDDGI MFGESAIWFKAGAAIFQEGGLNYLGNPSLIHAQNIVATLAVQVVLMGLVEGYRVNGGPAGEGLDPLYPGEAFDPLGLADD PEAFAELKVKEIKNGRLAMFACLGFFVQAIVTGKGPIENLTDHLANPAENNAFAYATKFTPQ Chlorophyll a-b binding protein of LHCII type 2, chloroplastic Dunaliella salina 0.023719543 2 LEVO EFYGPDRAKFLGPFSENDTPEYLTGEFPGDYGWDTAGLSADPQTFARYREIELIHARWALLGALGILTPELLSQYAGVQF GEPVWFKAGAQIFAAGGLNYLGNESLIHAQSIIATLAVQVVLMGLAEAYRANGGSEGFLDDLDTLYPGGAFDPLGLADDP DTFAELKVKEIKNGRLAMFSCLGFFVQAIVTGKGPVQNLTDHLADPTVNNAFASATKFTPG Chlorophyll a-b binding protein, chloroplastic, CP29 Dunaliella salina 0.021163662 2 LEVO SLSYLDGHLPGDMGFDPLHLSSPTV(SEP)LQIGVDEEDQNQAQNKKGDVEAIFRPEVFGLARFRETEVIHGRWAMLGTL GAIVGEAATGVSWVDAGKVELDGAQYLGQSLPFSISQLIWIEAILVGGVEVLRNNELDLEKRIYPGGAFDPLNLADEEDE EKSFRLKTAEIKHGRLAMVAFLGFGIQAAATGEGALGSLA Chlorophyll a-b binding protein, chloroplastic, CP26 Dunaliella salina 0.026233607 2 LEVO PDLEKWYGPDRKLFLPGGLLDRDDVPEYLNGELAGDYGYDPLGLGKDEEQVEKYRANELLHARWAMLAAAGIIIPEGLQA NGADIKGGTWFETGAEMLNGGTLNYFAVPFGVVQNPLPLAAVTLIEIVLLGAVEKFRVDGTGPAGFSPGVGKFDSDIFDG LDKLYPGGPFDPLNLADDPEVFAELQVKEIKNGRLAMIAVLAFAIQSYVTGEGPYANITKHLSDPFGYNLLTVLQGDDRV PTL Chlorophyll a-b binding protein of LHCII type 1, chloroplastic Dunaliella salina 0.023537566 2 LEVO SAWYGPDRPLFLGSLSGEPPSYLTGEFPGDYGWDTAGLSADPTTFARYRTIELIHARWALLGALGIITPELLAKNGVPFS EDGAIWFKAGAEIFKEGGLNYLGNENLIHAQSILATLAVQVIVMGAAEGFRANGEAPGVEGLDPLYPGGPFDPLGLADDP EAFAELKVKEIKNGRLAMFSCLGFFVQAIVTGKGPIQNLQDHLADPGVNNAFASATKFVPTP Photosystem II extrinsic protein U Dunaliella salina 0.003219625 2 LEVO QRVRTVLDMDDPAKEETVKELRKDINN CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX FE (II) ION 5.5845e-05 2 FE2 CHLORIDE ION 3.5453e-05 4 CL CHLOROPHYLL A 0.000893489 156 CLA PHEOPHYTIN A 0.0008712 4 PHO BETA-CAROTENE 0.000536873 16 BCR SODIUM ION 2.299e-05 2 NA 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 0.000704998 6 3PH (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol 0.000568871 2 C7Z 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 15 LMG DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 8 DGD 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 19 LHG DODECYL-BETA-D-MALTOSIDE 0.000510615 2 LMT 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 10 SQD SPHINGOSINE 0.000299492 4 SPH DIACYL GLYCEROL 0.000625018 6 DGA BICARBONATE ION 6.1017e-05 2 BCT 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 2 HEM (3R)-beta,beta-caroten-3-ol 0.0005528719999999999 2 RRX CHLOROPHYLL B 0.000907472 46 CHL (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 8 XAT PHOSPHATIDYLETHANOLAMINE 0.0007340389999999999 4 PTY (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate 0.00045355 2 LPX water 1.8015e-05 1724 HOH singleParticle particle 6.5 Quantifoil R1.2/1.3 COPPER 300 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 1.9000000000000001 GATAN K3 BIOQUANTUM (6k x 4k) 13586 51.81 1 401467 NONE C1 2.43 FSC 0.143 CUT-OFF 39357 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION 6KAC PDB experimental model AB INITIO MODEL