Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.

2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation_author em_admin em_author_list em_imaging _em_admin.last_update _em_imaging.microscope_model REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY audit_author chem_comp chem_comp_atom citation_author em_admin em_author_list em_imaging 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 pdbx_validate_close_contact struct_conn _chem_comp.formula _chem_comp_atom.pdbx_stereo_config _em_admin.last_update _em_imaging.microscope_model PDBe PDBe 2023-02-20 2024-03-06 2024-03-06 2026-09-16 Israel Science Foundation 199/21 Israel Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp. Fadeeva M Klaiman D Nelson N Nelson N Khozin-Goldberg I Zorin B Green alga, PSI, Coelastrella, membrane protein, Cryo-EM, PHOTOSYNTHESIS Fadeeva M Klaiman D Nelson N Khozin-Goldberg I Zorin B Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp. To Be Published 0353 8cmo FULLOVERLAP EMDB EMD-16732 associated EM volume

Coelastrella sp. Photosystem I Coelastrella sp. Photosystem I 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

Contains 11 core subunits and 10 antenna proteins

Coelastrella Chloroplast Thylakoid membrane 0.9 Photosystem I P700 chlorophyll a apoprotein A1 PsaA Coelastrella 0.082115883 1 LEVO KKVKIAVDRNPVETSFEKWAKPGHFSRTLSKGPNTTTWIWNLHADAHDFDSHTSDLEEISRKVFSAHFGQLGVIFIWLSG MYFHGARFSNYEAWLSDPVHIKPSAQVVWPVVGQEILNGDVGGGFQGIQITSGFFQLWRASGITSELQLYTTAIGGLVMA AAMFFAGWFHYHKAAPKLEWFQNVESMLNHHLAGLLGLGSLSWAGHQIHVSLPVNKLLDAGVDPKEIPLPHEFLLNRQIM QDLYPSFAKGLAPFFTLQWGEYSDFLTFNGGLNPVTGGLWLSDTAHHHLAIAVLFLVAGHMYRTNWGIGHSMKEILEAHK GPFTGEGHVGLYEILTTSWHAQLAINLALFGSLSIIVAHHMYSMPPYPYLATDYGTQLSLFTHHNWIGGFCIVGAGAHAA IFMVRDYDPTNNYNNLLDRVIRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQKT HFLAPQLTAPTALAATSATWGGDVVAVGGKVAMMPISLGTSDFLVHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLG FRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSLSIAIFHFSWKMQSDVWGTVTASGVSHITGGNFAQSANTINGWLRDFL WAQSSQVIQSYGSALSAYGLMFLGAHFVWAFSLMFLFSGRGYWQELIESIIWAHSKLKVAPSIQPRALSITQGRAVGVAH YLLGGIATTWSFFLARIIAV Photosystem I P700 chlorophyll a apoprotein A2 PsaB Coelastrella 0.08168060199999999 1 LEVO ATKLFPKFSQGLAQDPTTRRIWFGLAVAHDFESHDGMTEENLYQKIFASHFGQLAIIFLWTSGNLFHVAWQGNFEQWGAD PIHVRPIAHAIWDPHFGQPAVEAFTRGGASGPVNISTSGVYQWWYTIGMRTNQDLYVGSVFLALVSAIFLFASWLHLQPS FTPSLSWFKDAESRLNHHLSGLFGVSSLAWTGHLVHVAIPESRGKHVGWDNFLTQLPHPQGLTPFWTGNWAAYAQNPDSA SHVFGTSDGAGEAILTFLGGFHPQTQSLWLTDMAHHHLAIAVIFIVAGHMYRTNFGIGHRMSAILDAHVAPSGRLGAGHK GLFETVNNSLHFQLGLALASVGTICSLVAQHMYSLPPYAFLANDFTTQASLYTHHQYIAGFIMCGAFAHGAIFWIRDYDP EQNKGNVLARMLDHKEAIISHLSWVSLFLGFHTLGLYVHNDVMQAFGTPEKQILIEPVFAQWIQAAHGKAFYGFDLLLSS SSSSAASASQTLWLPGWLDAINNNQNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPCD GPGRGGTCDISAYDAFYLAVFWMLNTIGWVTFYFHWKHLTLWQGNVSQFDESSTYLMGWLRDYLWLNSSQLINGYNPFGM NSLSVWAWIFLFGHLVYATGFMFLISWRGYWQELIETLVWAHEKTPLANLVYWKDKPVALSIVQARLVGLTHFSVGYVFT YAAFLIASTSGK Photosystem I subunit VII PsaC Coelastrella 0.00878017 1 LEVO SHIVKIYDTCIGCTQCVRACPLDVLEMVPWNGCKANQMASAPRTEDCVGCKRCETACPTDFLSVRVYLGSESTRSMGLSY Photosystem I reaction center subunit II PsaD Coelastrella 0.016034349 1 LEVO WTEPTLNPDTPSPIFGGSTGGLLRKAQVEEFYVITWESNKEQIFEMPTGGAAIMRKGPNLLKFARKEQCLALTTQLRTKF KFTPCFYRVYPSGEVQYLHPKDGVYPEKVNAGRPGVNQNFRRIGENVNPIKVKFTGNGTMDI Photosystem I reaction center subunit IV PsaE Coelastrella 0.006850657 1 LEVO VGPKRGSQVKILRPESYWYNQTGKVVSVDQSGILYPVVVRFETQNYAGVTTNNFALDEVQP Photosystem I reaction center subunit III PsaF Coelastrella 0.01794968 1 LEVO DIAGLTPCSESAAYAKRLKNEVKGLNKRLKNYEADSAPAIALKATIERTQNRFANYAKAGLLCGADGLPHLISDPGLALK YGHAGEVFIPTFGFLYVAGWIGYVGRLYLNMVKGEAKPTEKEIIIDVPAALRLTWQGATWPVQVVAELRANTLTEKAENI TISPR Photosystem I reaction center subunit V PsaG Coelastrella 0.009806025 1 LEVO GLEPYLQVCAGTATMLAVGRFAFLPLHRRDLERSAATAGPKTTGSTYFDSLQQEASFITSTNDPAGFTLIDTMAWGALGH ALGFAFLAASSLQ Photosystem I reaction center subunit VIII PsaI Coelastrella 0.0043520749999999995 1 LEVO AAGSYPFVPPSWAPSVFVPLTGLVLPAIAMATLFVYIEKDN Photosystem I subunit IX PsaJ Coelastrella 0.00450828 1 LEVO MKNFTTYLSTAPVVALAWFTVTAALLIEINRFFPDPLVFS Photosystem I reaction center subunit X psaK Coelastrella 0.00879409 1 LEVO RADGFIGSTTNLIMVASTAAFLAAGKFGLAPTVKRGTDAACKLVDRPNAAGLISNDPSGFTAVDTLAFGALGHIAGVGIV LGLRATGNL Photosystem I reaction centre subunit XI PsaL Coelastrella 0.012735546 1 LEVO MLETPVTSTPEVASYLSNLPAYRTGVAPLLRGVEIGRAHGFFLPGPFIKLGPLRNVEGAAEIAGCLSAAGLVIILAAALS IYGSAMFQGEPRDPLQSAEGWNEFTSGFTVGALSGVAWAFACT Light-harvesting protein of photosystem I Lhca1 Coelastrella 0.02067143 2 LEVO RAGNWLPGSDAPAWLPDDLPGNYGFDPLGLCKDPASLKRFTESEVIHCRWAMLGAAGCLGVEALGFGNWYDAPLWAINGG SPTWFGISVPFDLNTLLAVEFVAMAAAESRRGDETDAAKRIYPGGAFDPLNFAKGDIETLKLKEIKNGRLAMMACLGFVA QHAATGKTPLQALGDHIGNPWGSNFATNGVSLPF Light-harvesting protein of photosystem I Lhca3 Coelastrella 0.023971211 1 LEVO QLYFTSESTLQYLDGTLPGDFGFDPLGLLDPVNSGGFVTPQWLAYSEVIHCRWAMLGAAGCIAPEILGKAGVGVDIRWFE TGVIPPAGTYDKYWTDPYSLFFIEVIAMQFAELRRWQDFKYPGSMSKQYFVGLEAVQGGSGDPAYPGGPWFNLFNLGAKS EADMKKLKLNEIKNGRLAMLAVFGYGAQAVLTGKGPYENLLDHLADPVNNNILTNFGK Light-harvesting protein of photosystem I Lhca7 Coelastrella 0.024091937999999997 1 LEVO AYGPDRPLWYPGNPAPAYLDGTLAGDYGFDPLGLSSDPETMRWMVHAELQNARWAMLGAAGVLLTSIGAAVGLPFPEWYE AGAAPLPSTVHGDWSFGTLTATMFLLFHWAEQKRIMDFRNPGSQGDGSFFGITDDFKSKENGYPGGRLFDPIGFSRGDEA MYKKYKQNEIVNGRLAMVANLGFWAQYAATGKGPIQNLADHLADPYHTTFTTNGVSVPFY Light-harvesting protein of photosystem I Lhca8 Coelastrella 0.022796273 1 LEVO RPLWMPGATVPAHLKGELAGDFGFDPLNLGKDPQALRWYQQAELVHGRTAMTAVAGILIPGLLTKAGVLNVPEWYEAGKV SAEQTGIALGPLLAVQLFMCGFVEGKRWMDFLKPGSQSEAGSFLGFEASFKGTDNGYPGGPFDPMGMCNESEAKTKDLKL KEIKNGRLAMLACLGFAAQYGATGKGPLDNLADHLAAPLKTTFVDNGISIPIHL Light-harvesting protein of photosystem I Lhca4 Coelastrella 0.022609793 1 LEVO ANRPSWFPGSKFPAHLDGTLPGDHGFDPLSLGVDPAKLKWYQQAELQNGRWAMLGAAGILVPDLLRAVGMGGPAAQVPWF EAGKYEYFAPPSALFASMMFLFAFVEFRRLQDIRKPGSANQDPIFTNNKLPAGEVGYPGGIFDPLGYSKGNMETLKLKEI KNARLAMLGFAGFVAQYQTTGKTPLQNLSDHLANPWSTTVLSNDLAR Light-harvesting protein of photosystem I Lhca5 Coelastrella 0.024988354999999997 1 LEVO DRKLWAPTVDSPSYLNGELAGDYGFDPLGLGADPVALKWYRQSELVHARWAMLGVAGVLGQEILRPDVFWYEAGEPQNLP GPFQNINMGGLLAWEFLLMHWVEVRRWQDYKNFGSVNEDPIFKGNKVPNPEMGYPGGIFDPLGFSKGNRKELQTKEIKNG RIAMIAFMSFVVQAQATGKGPLANLADHLSNPGANNWVSNINHCVTPSSVDVQGLTIPLTCLWPGS Light-harvesting protein of photosystem I Lhca6 Coelastrella 0.024911811 1 LEVO RPLWRPGSAPPAHLNGELPGDFGFDPLGLGANPESLKWFAESERVHARWAMLAVAGILVQEVVKPDVFWYDAPTKIDLPF NIVGLLAFEFFAMHFVELKRWQDFRNPGSVDADPLFPSNKLAPHEVGYPGFAPFVPGPMEELKVKEIKNGRLAMLAFIGF TMAAQVTGKGPLAALSEHLADPMGTTIFSKAVVVPGQVVQPECKIPQFTDFQGTKIFTPCLFQGLW Light-harvesting protein of photosystem I Lhca9 Coelastrella 0.020119057 1 LEVO RPTWLPNLNPPAHLKGEMAGDFGFDPLGLGADPARLKWFAEAEKTNGRWAMMAVVGILGQELLGVQPSWWNAGAKDYGVA MGPLTAMEFLIMGFLETKRYQGFKETGSSGLINQFPFDPAGMYSKDMAVKEVKNGRLAMVAFVGFAVQALASRTGPIEGL TKHLSNPGYNITYNLTHLQDVNTY Light-harvesting protein of photosystem I Lhca2 partial Coelastrella 0.007528819

partial

1 LEVO GRLAMLAFIGFCSQAAVRGKGPIDCLKDHIADPWNNNIYTSSVGKETCVTVALLCVWPIIIEATKSLNKG CHLOROPHYLL A ISOMER 0.000893489 1 CL0 CHLOROPHYLL A 0.000893489 213 CLA PHYLLOQUINONE 0.000450696 2 PQN BETA-CAROTENE 0.000536873 30 BCR 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 15 LHG (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate 0.00043652 2 NKP DIACYL GLYCEROL 0.000625018 1 DGA OCTANOIC ACID (CAPRYLIC ACID) 0.00014421100000000002 1 OCA IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 CALCIUM ION 4.0078e-05 1 CA DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 3 DGD (3R)-beta,beta-caroten-3-ol 0.0005528719999999999 1 RRX DODECYL-BETA-D-MALTOSIDE 0.000510615 5 LMT 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 2 LMG Phosphatidylinositol 0.000887128 1 T7X (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 LAURIC ACID 0.000200318 1 DAO (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 18 LUT CHLOROPHYLL B 0.000907472 22 CHL 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 1 SQD 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 0.000704998 4 3PH SPHINGOSINE 0.000299492 2 SPH (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate 0.00045355 1 LPX water 1.8015e-05 68 HOH singleParticle particle 2 8.0 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 12.0 PLASMA CLEANING 40 AIR 1.0

Harrick Plasma cleaner PDC-32G-2

ETHANE 90 295 LEICA EM GP

blot for 3 seconds before plunging.

Chlorophyll concentration was provided

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.15 1.75 130000.0 NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 31707 1.38 50.0 1 2972135 CTFFIND 4.1 NONE 2 C1 2.81 FSC 0.143 CUT-OFF RELION 167160 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 10 56000.0 emd_16732.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 325.5 325.5 325.5 90.0 90.0 90.0 X Y Z -0.012152449 0.031648654 0.000095737065 0.0013488486 0.651 0.651 0.651 0.007 AUTHOR ::::EMDATABANK.org::::EMD-16732:::: RIGID BODY FIT REAL 50.0 emd_16732_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 325.5 325.5 325.5 90.0 90.0 90.0 X Y Z -0.010679997 0.025383135 0.00009535876 0.0012925112 0.651 0.651 0.651 AUTHOR ::::EMDATABANK.org::::EMD-16732:::: emd_16732_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 325.5 325.5 325.5 90.0 90.0 90.0 X Y Z -0.011385646 0.025415206 0.000096115284 0.0012961943 0.651 0.651 0.651 AUTHOR ::::EMDATABANK.org::::EMD-16732::::