Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution

2026-09-30 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-03-12 2026-09-30 2026-09-30 2026-09-30 Germanys Excellence Strategy EXC 2008/1-390540038 Germany German Research Foundation (DFG) SFB1078 - TP A5 Germany Swedish Research Council 2019-03700_VR Sweden Formas 2019-01171_Formas Sweden Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution Gaullier G Boyka J Zouni A Blikstad C Monomeric Photosystem I, mPSI, photosynthesis Boyka J Gaullier G Blikstad C Zouni A Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution To Be Published 0353 EMD-10557 other EM volume EMD-10558 other EM volume EMD-10559 other EM volume 9qfp FULLOVERLAP PDB 6TRA unspecified PDB 6TRC unspecified PDB 6TRD unspecified EMDB EMD-10557 other EM volume EMDB EMD-10558 other EM volume EMDB EMD-10559 other EM volume EMDB EMD-53120 associated EM volume

Monomeric photosystem I Monomeric photosystem I 0 1 2 3 4 5 6 7 8 9 10 11

Endogeneous photosystem I complex purified from its native source organism Thermosynechococcus vestitus BP-1.

Thermosynechococcus vestitus BP-1 Photosystem I P700 chlorophyll a apoprotein A1 Thermosynechococcus vestitus BP-1 0.083267773 1 LEVO MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDTHTSDLEDISRKIFSAHFGHL AVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPIVGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYC TAIGGLVMAGLMLFAGWFHYHKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHHHLAIAVLFIIAGHMYRTNWG IGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINLAMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWI GGFLVVGGAAHGAIFMVRDYDPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHHIHAFTIHVTVLILLKGVLFA RSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLFWMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFA QSAITINGWLRDFLWAQASQVIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG P0A405 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Thermosynechococcus vestitus BP-1 0.083123648 1 LEVO MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWVSGSLFHVAWQGNFEQWVQD PVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGVYHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPK FRPSLSWFKNAESRLNHHLAGLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHSIKEMMDAKDFFGTKVEGPFN MPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLPPYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVR DYDPAQNKGNVLDRVLQHKEAIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDF GYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYWHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLIN GYNPFGTNNLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF SVGYILTYAAFLIASTAAKFG P0A407 1.97.1.12 Photosystem I iron-sulfur center Thermosynechococcus vestitus BP-1 0.008809207 1 LEVO MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSMGLA Y P0A415 1.97.1.12 Photosystem I reaction center subunit II Thermosynechococcus vestitus BP-1 0.015389494 1 LEVO MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLALAAQQLRPRKIND YKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQLKFTGKKPYDP P0A420 Photosystem I reaction center subunit IV Thermosynechococcus vestitus BP-1 0.008399485 1 LEVO MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNNFALHEVQEVAPPKKGK P0A423 Photosystem I reaction center subunit III Thermosynechococcus vestitus BP-1 0.017716586 1 LEVO MRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFERYSQALCGEDGLPHLVVDGRL SRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEIT VSPR P0A401 Photosystem I reaction center subunit VIII Thermosynechococcus vestitus BP-1 0.0042972340000000005 1 LEVO MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA P0A427 Photosystem I reaction center subunit IX Thermosynechococcus vestitus BP-1 0.004770698 1 LEVO MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL P0A429 Photosystem I reaction center subunit PsaK Thermosynechococcus vestitus BP-1 0.008483983 1 LEVO MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELLATTSFGHLLAAGVVSGLQYA GAL P0A425 Photosystem I reaction center subunit XII Thermosynechococcus vestitus BP-1 0.0034261149999999995 1 LEVO MALTDTQVYVALVIALLPAVLAFRLSTELYK P0A403 Photosystem I 4.8K protein Thermosynechococcus vestitus BP-1 0.004424317 1 LEVO MSTMATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK Q8DKP6 DODECYL-BETA-D-MALTOSIDE 0.000510615 16 LMT CHLOROPHYLL A 0.000893489 90 CLA PHYLLOQUINONE 0.000450696 2 PQN BETA-CAROTENE 0.000536873 19 BCR 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 5 LHG IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 CHLOROPHYLL A ISOMER 0.000893489 1 CL0 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 1 LMG MAGNESIUM ION 2.4305e-05 1 MG 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 1 SQD water 1.8015e-05 1183 HOH singleParticle particle 2.5 8.0 25.0 Tricin 25.0 NaCl sodium chloride 0.02 n-dodecyl-beta-D-maltoside Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 60 OTHER 0.04

Current 20 mA. Performed with a Pelco easiGlow device.

ETHANE 100 277 FEI VITROBOT MARK IV

Delay time 30 s Blot time 2 s Blot force 0 Drain time 0 s.

Concentration is expressed in mM chlorophyll.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.4 1.4000000000000001 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 22001 40.0 1 1000224

Topaz was trained with a manually picked set of 1010 particles.

cryoSPARC 4.5

Patch CTF estimation job in CryoSPARC, run with default settings.

PHASE FLIPPING AND AMPLITUDE CORRECTION Initial model computed from the particle images by an ab initio reconstruction job in CryoSPARC. C1 FOURIER SPACE 1.74 FSC 0.143 CUT-OFF cryoSPARC 4.5

Resolution as reported by CryoSPARC, using its mask auto-tightening procedure.

712866 MAXIMUM LIKELIHOOD cryoSPARC 4.5 MAXIMUM LIKELIHOOD cryoSPARC 4.5 4 cryoSPARC 4.5 emd_53120.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 331.776 331.776 331.776 90.0 90.0 90.0 X Y Z -0.51073664 1.4683826 0.00011664033 0.016124183 0.648 0.648 0.648 0.08 AUTHOR ::::EMDATABANK.org::::EMD-53120:::: Sharpened map from final non-uniform refinement in CryoSPARC. Sharpening B-factor from Guinier fit: -35.8. P0A405 A AlphaFold in silico model P0A407 B AlphaFold in silico model P0A415 C AlphaFold in silico model P0A420 D AlphaFold in silico model P0A423 E AlphaFold in silico model P0A401 F AlphaFold in silico model P0A427 I AlphaFold in silico model P0A429 J AlphaFold in silico model P0A425 K AlphaFold in silico model P0A403 M AlphaFold in silico model Q8DKP6 X AlphaFold in silico model FLEXIBLE FIT

Alphafold2 predictions fetched from AlphaFold-DB were placed into the map by rigid body fitting. Termini not supported by the map were trimmed. Every residue was visually inspected at least once, and its fit to density adjusted if necessary, using ISOLDE.

REAL emd_53120_msk_2.map emd_53120_msk_1.map emd_53120_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 331.776 331.776 331.776 90.0 90.0 90.0 X Y Z -0.0724958 0.36961985 0.00011664033 0.005547792 0.648 0.648 0.648 AUTHOR ::::EMDATABANK.org::::EMD-53120:::: Unfiltered, unsharpened map from final non-uniform refinement in CryoSPARC. emd_53120_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 331.776 331.776 331.776 90.0 90.0 90.0 X Y Z -0.09991491 0.440314 0.00018784945 0.010706982 0.648 0.648 0.648 AUTHOR ::::EMDATABANK.org::::EMD-53120:::: Half-map B from final non-uniform refinement in CryoSPARC. emd_53120_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 331.776 331.776 331.776 90.0 90.0 90.0 X Y Z -0.100841746 0.44990274 0.00018784634 0.010715639 0.648 0.648 0.648 AUTHOR ::::EMDATABANK.org::::EMD-53120:::: Half-map A from final non-uniform refinement in CryoSPARC.