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- EMDB-55898: Cryo-EM structure of Spinacia oleracea cytochrome b6f complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-55898
TitleCryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin
Map dataunfiltered main RELION map
Sample
  • Complex: cytochrome b6f complex incubated with plastocyanin
    • Protein or peptide: x 8 types
  • Protein or peptide: x 1 types
  • Ligand: x 9 types
Keywordsb6f complex / photosynthesis / membrane protein / electron transport / proton transport / quinone catalysis / plastocyanin / OXIDOREDUCTASE
Function / homology
Function and homology information


cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / : / cytochrome complex assembly / chloroplast thylakoid lumen / photosynthetic electron transport chain / : / chloroplast thylakoid membrane ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / : / cytochrome complex assembly / chloroplast thylakoid lumen / photosynthetic electron transport chain / : / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily ...: / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Iron-sulfur subunit PetC transmembrane anchor / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rudiment single hybrid motif / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cupredoxin
Similarity search - Domain/homology
Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Plastocyanin, chloroplastic / Cytochrome b6-f complex iron-sulfur subunit, chloroplastic / Cytochrome f / Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 6
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsPietras R / Sarewicz M / Szwalec M / Indyka P / Rawski M / Pintscher S / Mielecki B / Jaciuk M / Koziej L / Glatt S / Osyczka A
Funding support Poland, 2 items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-5B54/17-00 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Sci Adv / Year: 2023
Title: High-resolution cryo-EM structures of plant cytochrome bf at work.
Authors: Marcin Sarewicz / Mateusz Szwalec / Sebastian Pintscher / Paulina Indyka / Michał Rawski / Rafał Pietras / Bohun Mielecki / Łukasz Koziej / Marcin Jaciuk / Sebastian Glatt / Artur Osyczka /
Abstract: Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome bf (Cyt bf) is known as one of the key steps of photosynthesis, but the ...Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome bf (Cyt bf) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Q) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt bf homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Q in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt bf in one direction, transiently exposing the redox-active ring of quinone during catalysis. Our work proposes an unprecedented one-way traffic model that explains efficient quinol oxidation during photosynthesis and respiration.
History
DepositionDec 1, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55898.png

Downloads & links

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Map

FileDownload / File: emd_55898.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunfiltered main RELION map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-2.549382 - 4.536568
Average (Standard dev.)-0.000000000000167 (±0.046477076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55898_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution filtered main map used in figures

Fileemd_55898_additional_1.map
Annotationlocal resolution filtered main map used in figures
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_55898_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_55898_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : cytochrome b6f complex incubated with plastocyanin

EntireName: cytochrome b6f complex incubated with plastocyanin
Components
  • Complex: cytochrome b6f complex incubated with plastocyanin
    • Protein or peptide: Cytochrome b6
    • Protein or peptide: Cytochrome b6-f complex subunit 4
    • Protein or peptide: Cytochrome f
    • Protein or peptide: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
    • Protein or peptide: Cytochrome b6-f complex subunit 6
    • Protein or peptide: Cytochrome b6-f complex subunit 7
    • Protein or peptide: Cytochrome b6-f complex subunit 5
    • Protein or peptide: Cytochrome b6-f complex subunit 8
  • Protein or peptide: Plastocyanin, chloroplastic
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: UNDECYL-MALTOSIDE
  • Ligand: 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
  • Ligand: CHLOROPHYLL A
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: BETA-CAROTENE
  • Ligand: COPPER (II) ION

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Supramolecule #1: cytochrome b6f complex incubated with plastocyanin

SupramoleculeName: cytochrome b6f complex incubated with plastocyanin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Cytochrome b6

MacromoleculeName: Cytochrome b6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.186504 KDa
SequenceString: MSKVYDWFEE RLEIQAIADD ITSKYVPPHV NIFYCLGGIT LTCFLVQVAT GFAMTFYYRP TVTDAFASVQ YIMTEVNFGW LIRSVHRWS ASMMVLMMIL HVFRVYLTGG FKKPRELTWV TGVVLGVLTA SFGVTGYSLP WDQIGYWAVK IVTGVPDAIP V IGSPLVEL ...String:
MSKVYDWFEE RLEIQAIADD ITSKYVPPHV NIFYCLGGIT LTCFLVQVAT GFAMTFYYRP TVTDAFASVQ YIMTEVNFGW LIRSVHRWS ASMMVLMMIL HVFRVYLTGG FKKPRELTWV TGVVLGVLTA SFGVTGYSLP WDQIGYWAVK IVTGVPDAIP V IGSPLVEL LRGSASVGQS TLTRFYSLHT FVLPLLTAVF MLMHFLMIRK QGISGPL

UniProtKB: Cytochrome b6

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Macromolecule #2: Cytochrome b6-f complex subunit 4

MacromoleculeName: Cytochrome b6-f complex subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 17.456662 KDa
SequenceString:
MGVTKKPDLN DPVLRAKLAK GMGHNYYGEP AWPNDLLYIF PVVILGTIAC NVGLAVLEPS MIGEPADPFA TPLEILPEWY FFPVFQILR TVPNKLLGVL LMASVPAGLL TVPFLENVNK FQNPFRRPVA TTVFLVGTVV ALWLGIGATL PIDKSLTLGL F

UniProtKB: Cytochrome b6-f complex subunit 4

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Macromolecule #3: Cytochrome f

MacromoleculeName: Cytochrome f / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 31.35702 KDa
SequenceString: YPIFAQQGYE NPREATGRIV CANCHLANKP VDIEVPQAVL PDTVFEAVVR IPYDMQLKQV LANGKKGGLN VGAVLILPEG FELAPPDRI SPEMKEKMGN LSFQSYRPNK QNILVIGPVP GQKYSEITFP ILAPDPATKK DVHFLKYPIY VGGNRGRGQI Y PDGSKSNN ...String:
YPIFAQQGYE NPREATGRIV CANCHLANKP VDIEVPQAVL PDTVFEAVVR IPYDMQLKQV LANGKKGGLN VGAVLILPEG FELAPPDRI SPEMKEKMGN LSFQSYRPNK QNILVIGPVP GQKYSEITFP ILAPDPATKK DVHFLKYPIY VGGNRGRGQI Y PDGSKSNN TVYNSTATGI VKKIVRKEKG GYEINIADAS DGREVVDIIP RGPELLVSEG ESIKLDQPLT SNPNVGGFGQ GD AEVVLQD PLRIQGLLFF FASVILAQIF LVLKKKQFEK VQLSEMNF

UniProtKB: Cytochrome f

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Macromolecule #4: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

MacromoleculeName: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: plastoquinol-plastocyanin reductase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 18.95648 KDa
SequenceString:
ATSIPADNVP DMQKRETLNL LLLGALSLPT GYMLLPYASF FVPPGGGAGT GGTIAKDALG NDVIAAEWLK THAPGDRTLT QGLKGDPTY LVVESDKTLA TFGINAVCTH LGCVVPFNAA ENKFICPCHG SQYNNQGRVV RGPAPLSLAL AHCDVDDGKV V FVPWTETD FRTGEAPWWS A

UniProtKB: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

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Macromolecule #5: Cytochrome b6-f complex subunit 6

MacromoleculeName: Cytochrome b6-f complex subunit 6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 3.4522 KDa
SequenceString:
MFTLTSYFGF LLAALTITSA LFIGLNKIRL I

UniProtKB: Cytochrome b6-f complex subunit 6

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Macromolecule #6: Cytochrome b6-f complex subunit 7

MacromoleculeName: Cytochrome b6-f complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 3.774431 KDa
SequenceString:
NAAAEIFRIA AVMNGLTLVG VAIGFVLLRI EATVEE

UniProtKB: Cytochrome b6-f complex subunit 7

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Macromolecule #7: Cytochrome b6-f complex subunit 5

MacromoleculeName: Cytochrome b6-f complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 4.171985 KDa
SequenceString:
MIEVFLFGIV LGLIPITLAG LFVTAYLQYR RGDQLDL

UniProtKB: Cytochrome b6-f complex subunit 5

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Macromolecule #8: Cytochrome b6-f complex subunit 8

MacromoleculeName: Cytochrome b6-f complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 3.170809 KDa
SequenceString:
MDIVSLAWAA LMVVFTFSLS LVVWGRSGL

UniProtKB: Cytochrome b6-f complex subunit 8

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Macromolecule #9: Plastocyanin, chloroplastic

MacromoleculeName: Plastocyanin, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 10.420557 KDa
SequenceString:
VEVLLGGGDG SLAFLPGDFS VASGEEIVFK NNAGFPHNVV FDEDEIPSGV DAAKISMSEE DLLNAPGETY KVTLTEKGTY KFYCSPHQG AGMVGKVTVN

UniProtKB: Plastocyanin, chloroplastic

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Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #11: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 11 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #12: UNDECYL-MALTOSIDE

MacromoleculeName: UNDECYL-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 6 / Formula: UMQ
Molecular weightTheoretical: 496.589 Da
Chemical component information

ChemComp-UMQ:
UNDECYL-MALTOSIDE / detergent*YM

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Macromolecule #13: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 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
type: ligand / ID: 13 / Number of copies: 7 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

ChemComp-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

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 2 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #15: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 15 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #16: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 16 / Number of copies: 2 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #17: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 17 / Number of copies: 2 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #18: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration9.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3TRIS-HCL
15.0 mMNaClsodium chloride
0.7 mMC23H44O11n-undecyl beta-maltoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsfinal concentration of cytochrome b6f dimers and plastocyanin was 38.7 uM and 100 uM, respectively

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 7784 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 177412 / Details: template picker
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 87892
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Avg.num./class: 32532 / Software - Name: RELION (ver. 3.1.2) / Details: 3D classification
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7qrm

source_name: PDB, initial_model_type: experimental model

2pcf

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9tgg:
Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin

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