Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair

2026-08-12 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY 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_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp_atom.pdbx_stereo_config _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBj PDBc 2023-08-09 2024-06-19 2024-06-19 2026-08-12 National Natural Science Foundation of China (NSFC) 31925024 China Chinese Academy of Sciences YSBR-015 China Chinese Academy of Sciences XDB37020101 China Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair Li A Wang Y Liu Z monomeric Photosystem II, PSII repair, PHOTOSYNTHESIS Li A You T Pang X Wang Y Tian L Li X Liu Z Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Nat Commun UK 15 5211 5211 2024 38890314 doi:10.1038/s41467-024-49532-2 2041-1723 EMD-37265 consensus EM volume

Overall cryo-EM map of an intermediate-state complex during the process of photosystem II repair

EMD-37288 focused EM volume

Focused cryo-EM map of an intermediate-state complex during the process of photosystem II repair (Part1)

EMD-37289 focused EM volume

Focused cryo-EM map of an intermediate-state complex during the process of photosystem II repair (Part2)

8kde FULLOVERLAP EMDB EMD-37133 associated EM volume

Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair

EMDB EMD-37265 consensus EM volume

Overall cryo-EM map of an intermediate-state complex during the process of photosystem II repair

EMDB EMD-37288 focused EM volume

Focused cryo-EM map of an intermediate-state complex during the process of photosystem II repair (Part1)

EMDB EMD-37289 focused EM volume

Focused cryo-EM map of an intermediate-state complex during the process of photosystem II repair (Part2)

Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Chlamydomonas reinhardtii chloroplast Photosystem II CP47 reaction center protein Chlamydomonas reinhardtii 0.056089703 1 LEVO MGLPWYRVHTVVINDPGRLISVHLMHTALVSGWAGSMALFEISVFDPSDPVLNPMWRQGMFVLPFMTRLGITQSWGGWTI SGETATNPGIWSYEGVAAAHIILSGALFLASVWHWTYWDLELFRDPRTGKTALDLPKIFGIHLFLSGLLCFGFGAFHVTG VFGPGIWVSDPYGLTGSVQPVAPSWGADGFDPYNPGGIASHHIAAGILGVLAGLFHLCVRPSIRLYFGLSMGSIETVLSS SIAAVFWAAFVVAGTMWYGSAATPIELFGPTRYQWDQGFFQQEIQKRVQASLAEGASLSDAWSRIPEKLAFYDYIGNNPA KGGLFRTGAMNSGDGIAVGWLGHASFKDQEGRELFVRRMPTFFETFPVLLLDKDGIVRADVPFRKAESKYSIEQVGVSVT FYGGELDGLTFTDPATVKKYARKAQLGEIFEFDRSTLQSDGVFRSSPRGWFTFGHVCFALLFFFGHIWHGARTIFRDVFA GIDDDINDQVEFGKYKKLGDTSSLREAF A0A218N8S0 Photosystem II D2 protein Chlamydomonas reinhardtii 0.039474031 1 LEVO MTIAIGTYQEKRTWFDDADDWLRQDRFVFVGWSGLLLFPCAYFALGGWLTGTTFVTSWYTHGLATSYLEGCNFLTAAVST PANSMAHSLLFVWGPEAQGDFTRWCQLGGLWAFVALHGAFGLIGFMLRQFEIARSVNLRPYNAIAFSAPIAVFVSVFLIY PLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQA EETYSMVTANRFWSQIFGVAFSNKRWLHFFMLLVPVTGLWMSAIGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNIL LNEGIRAWMAAQDQPHERLVFPEEVLPRGNAL P06007 1.10.3.9 Cytochrome b559 subunit alpha Chlamydomonas reinhardtii 0.009312598 1 LEVO MAGKPVERPFSDILTSIRYWVIHSITVPALFIAGWLFVSTGLAYDVFGTPRPNEYFTEDRQEAPLITDRFNALEQVKKLS GN P48268 Cytochrome b559 subunit beta Chlamydomonas reinhardtii 0.004986013 1 LEVO MTTKKSAEVLVYPIFTVRWLAIHGIAVPTIFFLGAITAMQFIQR Q08363 Photosystem II reaction center protein H Chlamydomonas reinhardtii 0.009445063 1 LEVO MATGTSKAKPSKVNSDFQEPGLVTPLGTLLRPLNSEAGKVLPGWGTTVLMAVFILLFAAFLLIILEIYNSSLILDDVSMS WETLAKVS P22666 Photosystem II reaction center protein I Chlamydomonas reinhardtii 0.0042450349999999994 1 LEVO MLTLKIFVYTVVTFFVCLFIFGFLSNDPARNPGKNLD P59763 Photosystem II reaction center protein K Chlamydomonas reinhardtii 0.0050621419999999995 1 LEVO MTTLALVLAKLPEAYAPFAPIVDVLPVIPVFFILLAFVWQAAVSFR P18263 Photosystem II reaction center protein L Chlamydomonas reinhardtii 0.004431229 1 LEVO MARPNPNKQVVELNRTSLYWGLLLIFVLAVLFSSYIFN P32974 Photosystem II reaction center protein M Chlamydomonas reinhardtii 0.003762433 1 LEVO MEVNIYGLTATALFIIIPTSFLLILYVKTASTQD P92277 Photosystem II reaction center protein T Chlamydomonas reinhardtii 0.003639438 1 LEVO MEALVYTFLLVGTLGIIFFSIFFRDPPRMIK P37256 Photosystem II reaction center protein Ycf12 Chlamydomonas reinhardtii 0.003333058 1 LEVO MNIELALTLVSLVLVVSAGPLVVVLLSARGGNL P50370 Uncharacterized protein Chlamydomonas reinhardtii 0.009894716 1 LEVO MAAVCVSSKAVAVRPATRVASRPAARMVVRASAKPAQISEKAIAAGVSAAAAASLALAPIAEAAVTPSLKNFLGSLIAGA TVLGGIALAITAVSKFDKTIR A8I846 Photosystem II reaction center protein Z Chlamydomonas reinhardtii 0.006565863 1 LEVO MTSILQVALLALIFVSFALVVGVPVVFATPNGWTDNKGAVFSGLSLWLLLVFVVGILNSFVV P92276 Thylakoid enriched factor 14 (TEF14) Chlamydomonas reinhardtii 0.020601596 1 LEVO MALMMQKVAAPVSRRGMKVVAQATPNTASRRAILGVALLPALMYAPKALALIPDEEDEDLVEKAKANRRARLAQQRGVTR DFMASENLTDRRLEQELVPVQKAVYKLAKSGSQLESGDLKGAASTLSESWVGDFSTVASTVSGSTTAGKLVEAIKSVQAA AAKGDAAGSKRAYVSLVSDLQSWADASGLATSLKGL A8HY43 Photosystem II repair factor 1 (PRF1) Chlamydomonas reinhardtii 0.013340966 1 LEVO MLSNARAAVSKVHTSSAAVAPARPARVSHIVRASDKKLDERGVIAKDNSGRQNIFPTSSKAYYSSPTSSAVASSGLGGQQ GLGVLAAAFAIVALATAGVVLKQGDETLAQVNNAYQGDSLTVISSRIAESL A0A2K3DWM2 Photosystem II CP43 reaction center protein Chlamydomonas reinhardtii 0.050680737999999996 1 LEVO METLFNGTLTVGGRDQETTGFAWWSGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVSHFVPEKPMYEQGLILLPHI ATLGYGVGPGGEIIDTFPYFVSGVLHLISSAVLGFGGVYHSLIGPETLEESYPFFGYVWKDKNKMTNILGYHLIMLGLGA WLLVWKAMYFGGVYDTWAPGGGDVRVITNPTTNAAVIFGYLVKSPFGGDGWICSVDNMEDIIGGHIWIGTLEILGGIWHI YTTPWPWARRAFVWSGEAYLSYSLGAIGVMGFIACCMSWFNNTAYPSEFYGPTGPEASQSQAFTFLVRDQRLGANVASAQ GPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKLKNDIQPWQERRAAEYMTHAPLGSLNSVGGVAT EINAVNFVSPRSWLACSHFCLGFFFFIGHLWHAGRARAAAAGFEKGIDRFDEPVLSMRPLD P10898 Photosystem II protein D1 Chlamydomonas reinhardtii 0.03906634 1 LEVO MTAILERRENSSLWARFCEWITSTENRLYIGWFGVIMIPCLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIITG AVIPTSNAIGLHFYPIWEAASLDEWLYNGGPYQLIVCHFLLGVYCYMGREWELSFRLGMRPWIAVAYSAPVAAASAVFLV YPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFG QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVIGIWFTALGLSTMAFNLNGFNFNQSVVDSQGRVLNTWADI INRANLGMEVMHERNAHNFPLDLASTNSSSNN P07753 1.10.3.9 Photosystem II repair factor 2 (PRF2) Chlamydomonas reinhardtii 0.012002006999999999 1 LEVO MAALRCSVATRAAVPARRSSVVVRASTEQTTKRAMLGLLAGAVAGALLVAPAEAIRIPSHEFTGGMVKGGGSSPKSPTAA SMESYTLEGTKKQGVSLKTKKKLLAKVRENAQKSASS A8HNG8 CHLOROPHYLL A 0.000893489 35 CLA BETA-CAROTENE 0.000536873 10 BCR 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 6 LMG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 10 LHG 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 1 PL9 PHEOPHYTIN A 0.0008712 2 PHO PROTOPORPHYRIN IX CONTAINING FE 0.000616487 1 HEM RRR-ALPHA-TOCOPHERYLQUINONE 0.000446706 1 VTQ DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 3 DGD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 1 SQD BICARBONATE ION 6.1017e-05 1 BCT FE (II) ION 5.5845e-05 1 FE2 singleParticle particle 6.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 1.5 GATAN K2 SUMMIT (4k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.6 FSC 0.143 CUT-OFF 510932 PROJECTION MATCHING PROJECTION MATCHING emd_37133.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 332.8 332.8 332.8 90.0 90.0 90.0 X Y Z -0.9602674 61.421157999999998 0.0030603162 0.9954914 1.04 1.04 1.04 3.9 AUTHOR ::::EMDATABANK.org::::EMD-37133::::