2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_admin.last_update _pdbx_entry_details.has_protein_modification REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity 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 _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id PDBe PDBe 2022-02-02 2022-07-06 2022-07-06 2026-09-02 Biotechnology and Biological Sciences Research Council (BBSRC) BB/M011151/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/V006630/1 United Kingdom Leverhulme Trust RPG-2019-045 United Kingdom Wellcome Trust nr21005 United Kingdom 2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules Farmer DF Proctor MS Malone LA Swainsbury DPK Hawkings FR Hitchcock A Johnson MP Complex, cytochrome, membrane protein, electron transport, PHOTOSYNTHESIS Proctor MS Malone LA Farmer DA Swainsbury DJK Hawkings FR Pastorelli F Emrich-Mills TZ Siebert CA Hunter CN Johnson MP Hitchcock A Cryo-EM structures of the Synechocystis sp. PCC 6803 cytochrome b6f complex with and without the regulatory PetP subunit. Biochem.J. UK 479 1487 1503 2022 35726684 doi:10.1042/BCJ20220124 1470-8728 0043 BIJOAK 7r0w FULLOVERLAP EMDB EMD-14224 associated EM volume

2.8 Angstrom cryo-EM sructure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules

Cytochrome b6f complex in association with PetP Cytochrome b6f complex in association with PetP 0 1 2 3 4 5 6 7 8 9

strep-PetA used to purify cytochrome b6f complex from Synechocystis sp. PCC 6803. 6xHis-PetP recombinantly expressed in E. coli used to pull down cytochrome b6f complex and form the cytochrome b6f-PetP complex.

Synechocystis sp. PCC 6803 Uncharacterized protein Cp097, conserved in cyanobacteria Synechocystis PCC 6714 0.007231374 2 Escherichia coli BL21 LEVO MTIEIGQKVKVYRLRDRVSPDVVGKLGKVGVVKDFKMTDGSGIGAVVSFDDRTATWFFEDELKAI A0A068MZK2 Cytochrome b6 Synechocystis sp. PCC 6803 PCC 6803 / Kazusa 0.025075532999999997 2 LEVO MFSKEVTESKVFQWFNDRLEVQAISDDIASKYVPPHVNIFYCLGGLTLTCFLIQFATGFAMTFYYKPTVTEAFASVQYIM NEVNFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVVGVMLAVTTVTFGVTGYSLPWDQVGYWAVKIVSG VPAAIPVVGDQLVTLMRGSESVGQATLTRFYSLHTFVLPWAIAVLLLLHFLMIRKQGISGPL Q57038 Cytochrome b6-f complex subunit 4 Synechocystis sp. PCC 6803 PCC 6803 / Kazusa 0.017455783 2 LEVO MSIIKKPDLSDPDLRAKLAKGMGHNYYGEPAWPNDILYMFPICILGALGLIAGLAILDPAMIGEPADPFATPLEILPEWY LYPTFQILRILPNKLLGIAGMAAIPLGLMLVPFIESVNKFQNPFRRPIAMTVFLFGTAAALWLGAGATFPIDKSLTLGLF P27589 Cytochrome f Synechocystis sp. PCC 6803 PCC 6803 / Kazusa 0.03525933999999999 2 LEVO MRNPDTLGLWTKTMVALRRFTVLAIATVSVFLITDLGLPQAASAYPFWAQETAPLTPREATGRIVCANCHLAQKAAEVEI PQAVLPDTVFEAVVKIPYDLDSQQVLGDGSKGGLNVGAVLMLPEGFKIAPPDRLSEGLKEKVGGTYFQPYREDMENVVIV GPLPGEQYQEIVFPVLSPDPAKDKSINYGKFAVHLGANRGRGQIYPTGLLSNNNAFKAPNAGTISEVNALEAGGYQLILT TADGTETVDIPAGPELIVSAGQTVEAGEFLTNNPNVGGFGQKDTEVVLQNPTRIKFLVLFLAGIMLSQILLVLKKKQIEK VQAAELNF P26287 Cytochrome B6 Synechocystis sp. PCC 6803 0.0033761489999999997 2 LEVO MAAGVGIFIGYIAVFTGVTLGLLYGLRFVKLI A0A6P1VG96 Cytochrome b6-f complex subunit 7 Synechocystis sp. PCC 6803 PCC 6803 / Kazusa 0.003827555 2 LEVO MTAESMLANGAFIMIGLTLLGLAWGFVIIKLQGSEE P74810 Cytochrome b6-f complex subunit 5 Synechocystis sp. PCC 6803 PCC 6803 / Kazusa 0.004177004 2 LEVO MIEPLLLGIVLGLIPVTLAGLFVAAYLQYKRGNQFNLD P74149 Cytochrome b6-f complex subunit 8 Synechocystis sp. PCC 6803 PCC 6803 / Kazusa 0.003328965 2 LEVO MDILTLGWVSVLVLFTWSISMVVWGRNGF P72717 Rieske domain, PetC Synechocystis sp. PCC 6803 0.020562344 2 LEVO MLVKILKFRRFIMTQISGSPDVPDLGRRQFMNLLTFGTITGVAAGALYPAVKYLIPPSSGGSGGGVTAKDALGNDVKVTE FLASHNAGDRVLAQGLKGDPTYIVVQGDDTIANYGINAVCTHLGCVVPWNASENKFMCPCHGSQYNAEGKVVRGPAPLSL ALAHATVTDDDKLVLSTWTETDFRTDEDPWWA PROTOPORPHYRIN IX CONTAINING FE 0.000616487 6 HEM (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE 0.0007490069999999999 4 PGV beta,beta-caroten-4-one 0.000550856 2 ECH 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 2 PL9 CHLOROPHYLL A 0.000893489 2 CLA HEME C 0.0006205189999999999 2 HEC 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 1 LMG (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE 0.0007631 2 6PL (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol 0.000570927 1 2WA FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 2 SQD EICOSANE 0.000282547 1 LFA water 1.8015e-05 2 HOH singleParticle particle 4 7.6 25.0 Na3PO4 Sodium phosphate 10.0 MgCl2 Magnesium chloride 150.0 NaCl Sodium chloride 0.02 C56H92O25 glyco-diosgenin Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 25 ETHANE 70 288 LEICA EM GP

Sample was monodisperse but not present in every hole

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.2 2.4 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 20133 3.5 50.0 1 1169445 CTFFIND 4.1.14 PHASE FLIPPING AND AMPLITUDE CORRECTION

ab initio model generated from RELION's "initial model" job

1 C1 FOURIER SPACE 2.8 FSC 0.143 CUT-OFF RELION 3.1 152860 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 3 100000.0 RELION 3.1

After initial 3D refinement; no alignment classification

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