2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _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 PDBj 2024-05-06 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 PSII-PRF2' complex during the process of photosystem II repair Li A Liu Z Liu Z 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 8zee FULLOVERLAP EMDB EMD-60026 associated EM volume
Cryo-EM structure of an intermediate-state PSII-PRF2' complex during the process of photosystem II repair
 Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Chlamydomonas reinhardtii 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 Psb30 Chlamydomonas reinhardtii 0.003333058 1 LEVO MNIELALTLVSLVLVVSAGPLVVVLLSARGGNL P50370 4.1 kDa photosystem II subunit Chlamydomonas reinhardtii 0.009894716 1 LEVO MAAVCVSSKAVAVRPATRVASRPAARMVVRASAKPAQISEKAIAAGVSAAAAASLALAPIAEAAVTPSLKNFLGSLIAGA TVLGGIALAITAVSKFDKTIR A8I846 Photosystem II reaction center protein Z Chlamydomonas reinhardtii 0.006565863 1 LEVO MTSILQVALLALIFVSFALVVGVPVVFATPNGWTDNKGAVFSGLSLWLLLVFVVGILNSFVV P92276 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 0.036515551 1 LEVO NSSLWARFCEWITSTENRLYIGWFGVIMIPCLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVIPTSNAI GLHFYPIWEAASLDEWLYNGGPYQLIVCHFLLGVYCYMGREWELSFRLGMRPWIAVAYSAPVAAASAVFLVYPIGQGSFS DGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQEEETYNIV AAHGYFGRLIFQYASFNNSRSLHFFLAAWPVIGIWFTALGLSTMAFNLNGFNFNQSVVDSQGRVLNTWADIINRANLGME VMHERNAHN P07753 1.10.3.9 Chains: 1 Chlamydomonas reinhardtii 0.010153906999999998 1 LEVO MALTTLASRKAAAFSSVSSRKVALAPTPAKRMVSTRAVGDVNAPIEYAVGAAILVSLVATAIIPIVLNPGQQAADKIFNA KQKAPLDKPTTPGKNSGKK A8HMM7 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 8 LHG BICARBONATE ION 6.1017e-05 1 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 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 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 K3 (6k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 8KDE 2.9 FSC 0.143 CUT-OFF 159928 PROJECTION MATCHING MAXIMUM LIKELIHOOD emd_60026.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 280.80002 280.80002 280.80002 90.0 90.0 90.0 X Y Z -0.0036567594 0.21545635 -0.0001617863 0.0049706115 1.3500001 1.3500001 1.3500001 0.019 AUTHOR The cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle. emd_60026_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 280.80002 280.80002 280.80002 90.0 90.0 90.0 X Y Z -0.019567598 0.054678243 -0.000298985 0.002372383 1.3500001 1.3500001 1.3500001 AUTHOR The half cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle. emd_60026_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 280.80002 280.80002 280.80002 90.0 90.0 90.0 X Y Z -0.018780656 0.055327382 -0.00030131778 0.0023753173 1.3500001 1.3500001 1.3500001 AUTHOR The half cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle.