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6rqf

3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules

Method: ELECTRON MICROSCOPY Dmax: 130.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b6

OrganismNot specified

UniProt P00165

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain A； UniProt 1–215 Chain I； UniProt 1–215 Not recorded Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 1–215（215 aa）
Chain I 1–215（215 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–215（215 aa）
Chain I 1–215（215 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain A 1–215（215 aa）
Chain I 1–215（215 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–215（215 aa）
Chain I 1–215（215 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain A 1–215（215 aa）
Chain I 1–215（215 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain A 1–215（215 aa）
Chain I 1–215（215 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYB6_SPIOL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–215； UniProt 1–215 Author chain I； PDBConstruct 1–215； UniProt 1–215

Cytochrome b6-f complex subunit 4

OrganismNot specified

UniProt P00166

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain B； UniProt 1–160 Chain J； UniProt 1–160 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 1–160（160 aa）
Chain J 1–160（160 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 1–160（160 aa）
Chain J 1–160（160 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain B 1–160（160 aa）
Chain J 1–160（160 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 1–160（160 aa）
Chain J 1–160（160 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain B 1–160（160 aa）
Chain J 1–160（160 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain B 1–160（160 aa）
Chain J 1–160（160 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PETD_SPIOL
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–160； UniProt 1–160 Author chain J； PDBConstruct 1–160； UniProt 1–160

Cytochrome f

OrganismNot specified

UniProt P16013

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain C； UniProt 36–320 Chain K； UniProt 36–320 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain C 1–320（320 aa）
Chain K 1–320（320 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C 1–320（320 aa）
Chain K 1–320（320 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain C 1–320（320 aa）
Chain K 1–320（320 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C 1–320（320 aa）
Chain K 1–320（320 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain C 1–320（320 aa）
Chain K 1–320（320 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain C 36–320（285 aa）
Chain K 36–320（285 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYF_SPIOL
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–285； UniProt 36–320 Author chain K； PDBConstruct 1–285； UniProt 36–320

Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

OrganismNot specified

UniProt P08980

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain D； UniProt 52–230 Chain L； UniProt 52–230 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RFS RIESKE SOLUBLE FRAGMENT FROM SPINACH Deposited 1997-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 109–247（139 aa） Fragment：SOLUBLE FRAGMENT, C-TERMINAL RESIDUES 41 - 179
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.83 Å R-free 0.220
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain D 1–230（230 aa）
Chain L 1–230（230 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain D 1–230（230 aa）
Chain L 1–230（230 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain D 1–230（230 aa）
Chain L 1–230（230 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain D 1–230（230 aa）
Chain L 1–230（230 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain D 1–230（230 aa）
Chain L 1–230（230 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain D 52–230（179 aa）
Chain L 52–230（179 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UCRIA_SPIOL
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–179； UniProt 52–230 Author chain L； PDBConstruct 1–179； UniProt 52–230

Cytochrome b6-f complex subunit 6

OrganismNot specified

UniProt Q9M3L0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain E； UniProt 1–31 Chain M； UniProt 1–31 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain E 1–31（31 aa）
Chain M 1–31（31 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 1–31（31 aa）
Chain M 1–31（31 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain E 1–31（31 aa）
Chain M 1–31（31 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 1–31（31 aa）
Chain M 1–31（31 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain E 1–31（31 aa）
Chain M 1–31（31 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain E 1–31（31 aa）
Chain M 1–31（31 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PETL_SPIOL
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–31； UniProt 1–31 Author chain M； PDBConstruct 1–31； UniProt 1–31

Cytochrome b6-f complex subunit 7

OrganismNot specified

UniProt P80883

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain F； UniProt 1–36 Chain N； UniProt 1–36 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain F 1–36（36 aa）
Chain N 1–36（36 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain F 1–36（36 aa）
Chain N 1–36（36 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PETM_SPIOL
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 1–36； UniProt 1–36 Author chain N； PDBConstruct 1–36； UniProt 1–36

Cytochrome b6-f complex subunit 5

OrganismNot specified

UniProt P69461

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain G； UniProt 1–37 Chain O； UniProt 1–37 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 8 × 2 （P61045） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–37（37 aa）
Chain O 1–37（37 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain G 1–37（37 aa）
Chain O 1–37（37 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain G 1–37（37 aa）
Chain O 1–37（37 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain G 1–37（37 aa）
Chain O 1–37（37 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain G 1–37（37 aa）
Chain O 1–37（37 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain G 1–37（37 aa）
Chain O 1–37（37 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PETG_SPIOL
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–37； UniProt 1–37 Author chain O； PDBConstruct 1–37； UniProt 1–37

Cytochrome b6-f complex subunit 8

OrganismNot specified

UniProt P61045

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain H； UniProt 1–29 Chain P； UniProt 1–29 Not recorded Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 PL9 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.58 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6RQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H 1–29（29 aa）
Chain P 1–29（29 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 PL9 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 × 7 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–29（29 aa）
Chain P 1–29（29 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 PL9 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；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.
cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1
Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain H 1–29（29 aa）
Chain P 1–29（29 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain H 1–29（29 aa）
Chain P 1–29（29 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain H 1–29（29 aa）
Chain P 1–29（29 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric
Chain H 1–29（29 aa）
Chain P 1–29（29 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 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 × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PETN_SPIOL
Isoform —
PDB entities 8
Chains and sequence ranges Author chain H； PDBConstruct 1–29； UniProt 1–29 Author chain P； PDBConstruct 1–29； UniProt 1–29

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6rqf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6rqf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6rqf
Deposition date deposition_date2019-05-15
Structure title title3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules
Keywords keywordsPlastoquinol-plastocyanin oxido-reductase Cytochrome b6f Photosynthesis Electron transport, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.40 Å
Radius of gyration Rg (electron density) rg_electron41.92 Å
Forward intensity I(0) i0617375000.00
Molecular weight molecular_weight232200.0 kDa
Excluded volume excluded_volume301980 ų
Envelope volume envelope_volume403630 ų
Hydration-shell volume shell_volume77684 ų
Envelope diameter envelope_diameter141.0 Å
Shell Rg shell_rg48.92 Å
Envelope Rg envelope_rg42.11 Å
Shape Rg shape_rg41.91 Å
Total Rg total_rg42.36 Å
Total atoms total_atoms16359
Residues n_residues1944
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.6 Å
Rg (real space) rg_real43.25 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real6.1740e+08
I(0) uncertainty (real space) i0_real_error1.0920e+07
Rg (reciprocal space) rg_reciprocal43.40 Å
I(0) (reciprocal space) i0_reciprocal617500000.0000
Solution quality estimate total_estimate0.8661
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.4 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha64630000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.338
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (18)

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id6rqfA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id6rqfB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id6rqfB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily980 — plastocyanin oxidoreductase
Domain ID domain_id6rqfC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily830 — Cytochrome f large domain
Domain ID domain_id6rqfC02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
Domain ID domain_id6rqfI00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
Domain ID domain_id6rqfJ01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily510 — Single helix bin
Domain ID domain_id6rqfJ02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily980 — plastocyanin oxidoreductase
Domain ID domain_id6rqfK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily830 — Cytochrome f large domain
Domain ID domain_id6rqfK02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
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8. Citations (1)

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9. Files and Curves (10)