2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY audit_author citation citation_author _audit_author.identifier_ORCID _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year DATABASE_REFERENCES citation citation_author _citation.journal_volume _citation_author.name REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin _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 REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_chiral pdbx_validate_close_contact struct_conn struct_conn_type _chem_comp.formula _chem_comp_atom.pdbx_stereo_config _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBj PDBj 2022-02-16 2023-02-22 2023-02-22 2026-08-12 Japan Science and Technology JPMJCR13M4 Japan Ministry of Education, Culture, Sports, Science and Technology (Japan) Nanotechnology Platform Japan Kurisu G Gerle C membrane supercomplex, light harvesting, electron transport, green algae, PHOTOSYNTHESIS Gerle C Misumi Y Kawamoto A Tanaka H Kubota-Kawai H Tokutsu R Kim E Chorev D Abe K Robinson CV Mitsuoka K Minagawa J Kurisu G Biochim Biophys Acta Bioenerg NE 1864 148986 148986 2023 37270022 doi:10.1016/j.bbabio.2023.148986 1879-2650 7wyi FULLOVERLAP EMDB EMD-32892 associated EM volume

Native Photosystem I of Chlamydomonas reinhardtii

Native Photosystem I with bound Light Harvesting Complex I from Chlamydomonas reinhardtii thylakoid membranes. Native Photosystem I with bound Light Harvesting Complex I from Chlamydomonas reinhardtii thylakoid membranes. 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Membrane supercomplex purified without column use under green light conditions, stabilized by the mild detergent GDN with excess detergent removed using GraDeR.

Chlamydomonas reinhardtii Wild Type strain 137c Chloroplast Thylakoid membrane 0.765 Photosystem I P700 chlorophyll a apoprotein A1 Chlamydomonas reinhardtii 0.08323920299999998 1 LEVO MTISTPEREAKKVKIAVDRNPVETSFEKWAKPGHFSRTLSKGPNTTTWIWNLHADAHDFDSHTSDLEEISRKVFSAHFGQ LGIIFIWLSGMYFHGARFSNYEAWLSDPTHIKPSAQVVWPIVGQEILNGDVGGGFQGIQITSGFFQLWRASGITSELQLY TTAIGGLVMAAAMFFAGWFHYHKAAPKLEWFQNVESMLNHHLGGLLGLGSLAWAGHQIHVSLPVNKLLDAGVDPKEIPLP HDLLLNRAIMADLYPSFAKGIAPFFTLNWSEYSDFLTFKGGLNPVTGGLWLSDTAHHHVAIAVLFLVAGHMYRTNWGIGH SMKEILEAHRGPFTGEGHVGLYEILTTSWHAQLAINLALFGSLSIIVAHHMYAMPPYPYLATDYGTQLSLFTHHTWIGGF CIVGAGAHAAIFMVRDYDPTNNYNNLLDRVIRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQ PVFAQWIQNTHFLAPQLTAPNALAATSLTWGGDLVAVGGKVAMMPISLGTSDFMVHHIHAFTIHVTVLILLKGVLFARSS RLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSLSIVIFHFSWKMQSDVWGTVTASGVSHITGGNFAQSAN TINGWLRDFLWAQSSQVIQSYGSALSAYGLIFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPRALSI TQGRAVGVAHYLLGGIATTWSFFLARIISVG P12154 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Chlamydomonas reinhardtii 0.082184266 1 LEVO MATKLFPKFSQGLAQDPTTRRIWYGLAMAHDFESHDGMTEENLYQKIFASHFGQLSIIFLWTSGNLFHVAWQGNFEQWVT DPVHIRPIAHAIWDPHFGQPAVEAFTRGGASGPVNISTSGVYQWWYTIGMRTNQDLYVGSVFLALVSAIFLFAGWLHLQP NFQPSLSWFKDAESRLNHHLSGLFGVSSLAWTGHLVHVAIPESRGQHVGWDNFLSVLPHPQGLTPFFTGNWAAYAQSPDT ASHVFGTAQGSGQAILTFLGGFHPQTQSLWLTDMAHHHLAIAVIFIVAGHMYRTNFGIGHRMQAILEAHTPPSGSLGAGH KGLFDTVNNSLHFQLGLALASVGTITSLVAQHMYSLPPYAFQAIDFTTQAALYTHHQYIAGFIMCGAFAHGAIFFIRDYD PEQNKGNVLARMLDHKEALISHLSWVSLFLGFHTLGLYVHNDVMQAFGTPEKQILIEPVFAQWIQAAHGKALYGFDFLLS SKTSAAFANGQSLWLPGWLDAINNNQNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPC DGPGRGGTCDISAYDAFYLAVFWMLNTIGWVTFYWHWKHLTLWQGNVAQFDESSTYLMGWLRDYLWLNSSQLINGYNPFG MNSLSVWAWTFLFGHLIYATGFMFLISWRGYWQELIETLVWAHEKTPLANLVYWKDKPVALSIVQARLVGLAHFSVGYIF TYAAFLIASTSGRFG P09144 1.97.1.12 Photosystem I iron-sulfur center Chlamydomonas reinhardtii 0.008869325 1 LEVO MAHIVKIYDTCIGCTQCVRACPLDVLEMVPWDGCKASQMASAPRTEDCVGCKRCETACPTDFLSVRVYLGSESTRSMGLS Y Q00914 1.97.1.12 Photosystem I reaction center subunit II, chloroplastic Chlamydomonas reinhardtii 0.021372886999999997 1 LEVO MAVMMRTQAPAATRASSRVAVAARPAARRAVVVRAEAEAAPAAAKKAAEKPAWTVPTLNPDTPSPIFGGSTGGLLRKAQT EEFYVITWEAKKEQIFEMPTGGAAIMRQGPNLLKFGKKEQCLALTTQLRNKFKLTPCFYRVFPDGKVQYLHPADGVYPEK VNAGRVGANQNMRRIGQNVNPIKVKFSGRMMSPAEI Q39615 Photosystem I reaction center subunit IV, chloroplastic Chlamydomonas reinhardtii 0.010786395 1 LEVO MQALSSRVNIAAKPQRAQRLVVRAEEVKAAPKKEVGPKRGSLVKILRPESYWFNQVGKVVSVDQSGVRYPVVVRFENQNY AGVTTNNYALDEVVAAK P12352 Photosystem I reaction center subunit III, chloroplastic Chlamydomonas reinhardtii 0.024088936000000002 1 LEVO MALTMRNPAVKASSRVAPSSRRALRVACQAQKNETASKVGTALAASALAAAVSLSAPSAAMADIAGLTPCSESKAYAKLE KKELKTLEKRLKQYEADSAPAVALKATMERTKARFANYAKAGLLCGNDGLPHLIADPGLALKYGHAGEVFIPTFGFLYVA GYIGYVGRQYLIAVKGEAKPTDKEIIIDVPLATKLAWQGAGWPLAAVQELQRGTLLEKEENITVSPR P12356 Photosystem I reaction center subunit IX Chlamydomonas reinhardtii 0.004750509 1 LEVO MKDFTTYLSTAPVIATIWFTFTAGLLIEINRYFPDPLVFSF P59777 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.023520697 1 LEVO MRTLSARTAAPRGFSGRRVAAVSNGSRVTMKAGNWLPGSDAPAWLPDDLPGNYGFDPLSLGKEPASLKRFTESEVIHGRW AMLGVAGSLAVELLGYGNWYDAPLWAVNGGKATWFGIEVPFDLNALLAFEFVAMAAAEGQRGDAGGVVYPGGAFDPLGFA KDSSKSGELKLKEIKNGRLAMVAFLGFVAQHAATGKGPIAALGEHLANPWGANFATNGISVPFF Q7DM26 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.032629486 1 LEVO MMLTKSAQAAFSGKVARPAKANRARLVCRAEEKSIAKVDRSKDQLYVGASQSSLAYLDGSLPGDFGFDPLGLLDPVNSGG FIEPKWLQYSEVIHARWAMLGAAGCIAPEVLGAAGLIPDATNIKWFESGVIPPAGSYNGYWADPYTIFFVEIVAMQFAEL RRLQDFRYPGSMGQQYFLGLEAIFKGSGDAAYPGGPFFNLFNLGKTEAAMKELKLKEIKNGRLAMLAMLGYGAQAVMTGK GPFQNLVEHLADPVNNNILTNFAGRVSGSSQPWRPHGWWRRRYRSVAALALIRNRSVC A8JF10 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.026248868999999998 1 LEVO MALSMIAQRRAGAFSARQAPRAVRAQAAVRPVWFPGNPPPAHLDGSLAGDYGFDPLFLGQEPQTLKWYVQAELVHGRFAM LGAAGIILTSIGAKVGLGFPEWYDAGKVVVEKNNIDFPTLMVIQFYLMGWAETKRWYDFKNPGSQADGSFLGFTEEFKGL ENGYPGGRFFDPMGLSRGDAAKYQEYKQKEVKNGRLAMIACLGFAAQYAATGKGPLDNLADHLADPNHVNFATNGVSIPI A Q84Y02 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.025948812 1 LEVO MALTMKRSGVAARSASSRKSVVTCVARQSWLPGSQIPAHLDTPAAQALAGNFGFDPLGLGKDPVALRWYQQAELIHCRTA MAGVAGILIPGLLTKAGALNVPEWYDAGKVAIENSFAPWGSLLAVQLFLCGFVEAKRWQDIRKPGSQGEPGSFLGFEASL KGTSELGYPGGPFDPLGLSKEADKWADWKLKEVKNGRLAMLAFLGFVAQKYATGAGPVDNLAAHLKDPWHVNYATNGVSL PFL Q75VY7 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.023923205 1 LEVO MALSMRTLSARTAAPRGFSGRRVAAVSNGSRVTMKAGNWLPGSDAPAWLPDDLPGNYGFDPLSLGKEPASLKRFTESEVI HGRWAMLGVAGSLAVELLGYGNWYDAPLWAVNGGKATWFGIEVPFDLNALLAFEFVAMAAAEGQRGDAGGVVYPGGAFDP LGFAKDSSKSGELKLKEIKNGRLAMVAFLGFVAQHAATGKGPIAALGEHLANPWGANFATNGISVPFF Q05093 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.028729822 1 LEVO MAFVLAKSSAFGVAAKPVSRRSSVAVKASAVPENVKEAREWIDAWKSKSGGAKRDAALPSWMPGADLPGYLNGTLPGDFG FDPLYLGQDPVKLKWYAQAELMNARFAMLAVAGILVPELLSNIGFSWPGAGVAWYDAGKFEYFAPASSLFGVQMLLFAWV EIRRYQDFVKPGSANQDPIFTNNKLPDGNEPGYPGGIFDPFGWSKGDIKSLKLKEIKNGRLAMLAFAGFIGQAYTTGTTP LKNLSTHLADPWSTTVWQNDLARL Q75VZ0 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.028257555 1 LEVO MAALMQKSALSRPACSTRSSRRAVVVRAAADRKLWAPGVVAPEYLKGDLAGDYGWDPLGLGADPTALKWYRQSELQHARW AMLGVAGVLVQEIVKPDVYFYEAGLPQNLPEPFTNINMGGLLAWEFILMHWVEVRRWQDYKNFGSVNEDPIFKGNKVPNP EMGYPGGIFDPFGFSKGNLKELQTKEIKNGRLAMIAYMAFILQAQATGKGPLAALSAHLSNPFGNNILKNIGTCTVPHSV DVQGLTIPLTCLWPGSQ Q75VY8 Chlorophyll a-b binding protein, chloroplastic Chlamydomonas reinhardtii 0.027812372999999998 1 LEVO MMLVAKNAVAARPSARSARRSVVAKASSRPLWLPGSTPPAHLKGDLPGDFGFDPLGLGANAESLKWFKESELVHSRWAMA AVAGILVQEIVRPDVFWYNAGKEVESPLGPLGLLAVEFFLMHWVEVRRWQDLRKPGSVDQDPIFSQYKLPPHEVGYPGGV FAPFIPGDLAELKVKEIKNGRLAMLAFVGFVMAAQVTGKGPIAALQEHLADPWGTTIFSKAAVVPGQAVAPPCKIPASVS YKGIEIPTPCFLQGLWP Q75VY6 CHLOROPHYLL A ISOMER 0.000893489 1 CL0 CHLOROPHYLL A 0.000893489 155 CLA PHYLLOQUINONE 0.000450696 2 PQN IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 CHLOROPHYLL B 0.000907472 10 CHL singleParticle particle 7.0 6.5 25.0 C6H13NO4S MES 0.02 C56H92O25 GDN Quantifoil R1.2/1.3 MOLYBDENUM 200

Both sides of the grid were glow discharged at 5 mA for 90 seconds.

ETHANE 95 277 FEI VITROBOT MARK IV

2.6 microliter of sample were applied to cryo-grids and blotted for 4 seconds using Whatman #1 before plunge freezing..

The sample was monodisperse with a low level of contaminants and excess free detergent removed using the GraDeR approach.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.25 2.5 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN

Preliminary grid screening was performed manually using a JEOL JEM-3000SFF microscope.

FEI FALCON II (4k x 4k) INTEGRATING 4096 4096 1-16 1 4080 2.0 45.5 1 1410677 Gctf PHASE FLIPPING ONLY

Stochastic gradient descent as implemented in cryoSPARC

3.9 FSC 0.143 CUT-OFF cryoSPARC 2 47618 MAXIMUM LIKELIHOOD cryoSPARC 2

As implemented in cryoSPARC

MAXIMUM LIKELIHOOD cryoSPARC 2 cryoSPARC 2 6JO5 PDB experimental model RIGID BODY FIT Correlation coefficient