Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_entry_details.has_protein_modification REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update 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 STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight PDBe PDBe 2022-05-25 2023-01-25 2023-01-25 2026-09-02 Foundation for Polish Science POIR.04.04.00-00-5B54/17-00 Poland Foundation for Polish Science TEAM TECH CORE FACILITY/2017-4/6 Poland Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Sarewicz M Szwalec M Pintscher S Indyka P Rawski M Pietras R Mielecki B Koziej L Jaciuk M Glatt S Osyczka A cytochrome, Spinacia oleracea, plastoquinones, cryo-EM, PHOTOSYNTHESIS Sarewicz M Szwalec M Pintscher S Indyka P Rawski M Pietras R Mielecki B Koziej L Jaciuk M Glatt S Osyczka A High-resolution cryo-EM structures of plant cytochrome b 6 f at work. Sci Adv US 9 eadd9688 eadd9688 2023 36638176 doi:10.1126/sciadv.add9688 2375-2548 EMD-14123 other EM volume

7QRM contains the same protein complex with plastocyanin

7zyv FULLOVERLAP PDB 7QRM re-refinement

7QRM contains the same protein complex with plastocyanin

EMDB EMD-14123 other EM volume

7QRM contains the same protein complex with plastocyanin

EMDB EMD-15027 associated EM volume

Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution

Cytochrome b6f complex Cytochrome b6f complex 0 1 2 3 4 5 6 7 8 9 Spinacia oleracea Leaves Chloroplasts thylakoids 0.22 Cytochrome b6 Spinacia oleracea 0.024186504 2 LEVO MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRPTVTDAFASVQYIMTEVNFGW LIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVTGVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPV IGSPLVELLRGSASVGQSTLTRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL P00165 Cytochrome b6-f complex subunit 4 Spinacia oleracea 0.017456661999999998 2 LEVO MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPSMIGEPADPFATPLEILPEWY FFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKFQNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF P00166 Cytochrome f Spinacia oleracea 0.035355663999999995 2 LEVO MQTINTFSWIKEQITRSISISLILYIITRSSIANAYPIFAQQGYENPREATGRIVCANCHLANKPVDIEVPQAVLPDTVF EAVVRIPYDMQLKQVLANGKKGGLNVGAVLILPEGFELAPPDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPGQKYSE ITFPILAPDPATKKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVKKIVRKEKGGYEINIADASDGREVVD IIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEVVLQDPLRIQGLLFFFASVILAQIFLVLKKKQFEKVQLSEMNF P16013 Cytochrome b6-f complex iron-sulfur subunit, chloroplastic Spinacia oleracea 0.024347898 2 LEVO MASFTLSSATPSQLCSSKNGMFAPSLALAKAGRVNVLISKERIRGMKLTCQATSIPADNVPDMQKRETLNLLLLGALSLP TGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWLKTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTH LGCVVPFNAAENKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA P08980 7.1.1.6 Cytochrome b6-f complex subunit 6 Spinacia oleracea 0.0034521999999999995 2 LEVO MFTLTSYFGFLLAALTITSALFIGLNKIRLI Q9M3L0 Cytochrome b6-f complex subunit 7 Spinacia oleracea 0.012953799999999998 2 LEVO MATAAASTTLSSAAVPAISGSRGQRKMNKVVYMSGVNSYGGLKANNAVLGLGQAVCTEQCFANVVSSLRSTATKKGRSGG GGGAGGGALTSTCNAAAEIFRIAAVMNGLTLVGVAIGFVLLRIEATVEEAE A0A0K9RMM1 Cytochrome b6-f complex subunit 5 Spinacia oleracea 0.004171985 2 LEVO MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL P69461 Cytochrome b6-f complex subunit 8 Spinacia oleracea 0.003170809 2 LEVO MDIVSLAWAALMVVFTFSLSLVVWGRSGL P61045 Thylakoid soluble phosphoprotein Spinacia oleracea 0.010608004 2 LEVO MSSLPFVFGAAASSRVVTAAAAKGTAETKQEKSFVDWLLGKITKEDQFYETDPILRGGDVKSSGSTSGKKGGTTSGKKGT VSIPSKKKNGNGGVFGGLFAKKD Q8GT36 PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM HEME C 0.0006205189999999999 4 HEC CHLOROPHYLL A 0.000893489 2 CLA UNDECYL-MALTOSIDE 0.000496589 10 UMQ 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 6 PL9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 2 SQD FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES BETA-CAROTENE 0.000536873 2 BCR singleParticle particle 6.2 8.0 10.0 2-Amino-2-(hydroxymethyl)propane-1,3-diol Tris 15.0 NaCl sodium chloride 0.8 (2R,3R,4S,5S,6R)-2-[(2R,3S,4R,5R,6R)-4,5-dihydroxy-2-(hydroxymethyl)-6-undecoxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol undecyl maltoside

Buffer and the diluted protein sample were filtered through a 0.22 um syringe filter. Prior to freezing, protein sample was concentrated on centrifugal filter units with 50K MWCO.

Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE 60 AIR 30.0 ETHANE 100 277 FEI VITROBOT MARK IV

blot time 2 s, wait time 0 s, blot force -1.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.9 2.1 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 7651 1.82 40.0 1

20 eV slit, fully tuned before the experiment

42951

given number of particles is after blob picker and 2D cleaning

cryoSPARC v3.3.1 patch CTF, global and local CTF refinement

Non-uniform Refinement with iterative global CTF refinement and anisotropic magnification fitting

PHASE FLIPPING AND AMPLITUDE CORRECTION 7QRM C2 2.13 FSC 0.143 CUT-OFF cryoSPARC v3.3.1 Non-uniform Refinement

Non-uniform Refinement

685979 MAXIMUM LIKELIHOOD cryoSPARC v3.3.1 Ab-Initio Reconstruction

Ab-Initio Reconstruction

ANGULAR RECONSTITUTION cryoSPARC v3.3.1 Non-uniform Refinement

Non-uniform Refinement

3 233000.0 cryoSPARC v3.3.1 Ab-Initio Reconstruction

asymmetric division of particles with a structural differences visible, 375k vs 312k vs 9.8k

emd_15027.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 372 372 372 0 0 0 372 372 372 319.92 319.92 319.92 90.0 90.0 90.0 X Y Z -0.577109 2.4545486 0.0013920823 0.04171142 0.86 0.86 0.86 0.208 AUTHOR ::::EMDATABANK.org::::EMD-15027:::: 7QRM PDB experimental model RIGID BODY FIT emd_15027_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 372 372 372 0 0 0 372 372 372 319.92 319.92 319.92 90.0 90.0 90.0 X Y Z -4.943528 12.250247999999999 0.0013920822 0.13821971 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-15027:::: sharpened map emd_15027_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 372 372 372 0 0 0 372 372 372 319.92 319.92 319.92 90.0 90.0 90.0 X Y Z -0.56376827 2.7636182 0.002062716 0.050990447 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-15027:::: emd_15027_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 372 372 372 0 0 0 372 372 372 319.92 319.92 319.92 90.0 90.0 90.0 X Y Z -0.6410727 2.718234 0.0020729739 0.051007275 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-15027::::