9TGG | pdb_00009tgg

Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin

PDB DOI: https://doi.org/10.2210/pdb9TGG/pdb
EM Map EMD-55898: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Spinacia oleracea
Mutation(s): No

Deposited: 2025-12-01 Released: 2025-12-17
Deposition Author(s): Pietras, R., Sarewicz, M., Szwalec, M., Indyka, P., Rawski, M., Pintscher, S., Mielecki, B., Jaciuk, M., Koziej, L., Glatt, S., Osyczka, A.
Funding Organization(s): Foundation for Polish Science

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

High-resolution cryo-EM structures of plant cytochrome b6f at work

Sarewicz, M., Szwalec, M., Pintscher, S., Indyka, P., Rawski, M., Pietras, R., Mielecki, B., Koziej, L., Jaciuk, M., Glatt, S., Osyczka, A.

(2023) Sci Adv 9: eadd9688

PubMed: 36638176 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.add9688
Primary Citation Related Structures:
7QRM, 7ZYV, 9TGG

PubMed Abstract:
Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome b ₆f (Cyt b ₆f) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Q _p) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt b ₆f homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Q _p in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt b ₆f 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.

Organizational Affiliation

Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland.

Macromolecule Content

Total Structure Weight: 241.51 kDa
Atom Count: 16,731
Modeled Residue Count: 2,001
Deposited Residue Count: 2,043
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6	A, I	215	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P00165 (Spinacia oleracea) Explore P00165 Go to UniProtKB: P00165
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00165
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 4	B, J	160	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P00166 (Spinacia oleracea) Explore P00166 Go to UniProtKB: P00166
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00166
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome f	C, K	285	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P16013 (Spinacia oleracea) Explore P16013 Go to UniProtKB: P16013
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16013
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex iron-sulfur subunit, chloroplastic	D, L	179	Spinacia oleracea	Mutation(s): 0 EC: 7.1.1.6
UniProt
Find proteins for P08980 (Spinacia oleracea) Explore P08980 Go to UniProtKB: P08980
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08980
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 6	E, M	31	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for Q9M3L0 (Spinacia oleracea) Explore Q9M3L0 Go to UniProtKB: Q9M3L0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M3L0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 7	F, N	36	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P80883 (Spinacia oleracea) Explore P80883 Go to UniProtKB: P80883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80883
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 5	G, O	37	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P69461 (Spinacia oleracea) Explore P69461 Go to UniProtKB: P69461
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69461
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b6-f complex subunit 8	H, P	29	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P61045 (Spinacia oleracea) Explore P61045 Go to UniProtKB: P61045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61045
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastocyanin, chloroplastic	Q	99	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P00289 (Spinacia oleracea) Explore P00289 Go to UniProtKB: P00289
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00289
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain NA [auth J] MOL2 format, chain X [auth A] MOL2 format, chain NA [auth J] mmCIF format, chain X [auth A] mmCIF format, chain NA [auth J]	NA [auth J], X [auth A]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain NA [auth J] Focus chain X [auth A] Interactions & Density Focus chain NA [auth J] Focus chain X [auth A]
SQD (Subject of Investigation/LOI) Query on SQD Download:Ideal Coordinates CCD File SDF format, chain QA [auth K] SDF format, chain CA [auth D] MOL2 format, chain QA [auth K] MOL2 format, chain CA [auth D] mmCIF format, chain QA [auth K] mmCIF format, chain CA [auth D]	CA [auth D], QA [auth K]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C₄₁ H₇₈ O₁₂ S RVUUQPKXGDTQPG-JUDHQOGESA-N		Interactions Focus chain CA [auth D] Focus chain QA [auth K] Interactions & Density Focus chain CA [auth D] Focus chain QA [auth K]
PL9 (Subject of Investigation/LOI) Query on PL9 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth A] SDF format, chain W [auth A] SDF format, chain OA [auth J] SDF format, chain MA [auth I] SDF format, chain LA [auth I] SDF format, chain FA [auth I] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain W [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain MA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain FA [auth I] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain W [auth A] mmCIF format, chain OA [auth J] mmCIF format, chain MA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain FA [auth I]	FA [auth I] LA [auth I] MA [auth I] OA [auth J] W [auth A] FA [auth I], LA [auth I], MA [auth I], OA [auth J], W [auth A], Y [auth A], Z [auth B]	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 C₅₃ H₈₀ O₂ FKUYMLZIRPABFK-UHFFFAOYSA-N		Interactions Focus chain FA [auth I] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain OA [auth J] Focus chain W [auth A] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth I] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain OA [auth J] Focus chain W [auth A] Focus chain Y [auth A] Focus chain Z [auth B]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain PA [auth K] SDF format, chain IA [auth I] SDF format, chain AA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain PA [auth K] MOL2 format, chain IA [auth I] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain PA [auth K] mmCIF format, chain IA [auth I] mmCIF format, chain AA [auth C]	AA [auth C], IA [auth I], PA [auth K], T [auth A]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain AA [auth C] Focus chain IA [auth I] Focus chain PA [auth K] Focus chain T [auth A] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth I] Focus chain PA [auth K] Focus chain T [auth A]
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain HA [auth I] SDF format, chain GA [auth I] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain HA [auth I] MOL2 format, chain GA [auth I] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain HA [auth I] mmCIF format, chain GA [auth I]	GA [auth I], HA [auth I], R [auth A], S [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain GA [auth I] Focus chain HA [auth I] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain GA [auth I] Focus chain HA [auth I] Focus chain R [auth A] Focus chain S [auth A]
BCR (Subject of Investigation/LOI) Query on BCR Download:Ideal Coordinates CCD File SDF format, chain SA [auth P] SDF format, chain EA [auth H] MOL2 format, chain SA [auth P] MOL2 format, chain EA [auth H] mmCIF format, chain SA [auth P] mmCIF format, chain EA [auth H]	EA [auth H], SA [auth P]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain EA [auth H] Focus chain SA [auth P] Interactions & Density Focus chain EA [auth H] Focus chain SA [auth P]
UMQ Query on UMQ Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain TA [auth P] SDF format, chain KA [auth I] SDF format, chain JA [auth I] SDF format, chain DA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth P] MOL2 format, chain KA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain DA [auth E] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth P] mmCIF format, chain KA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain DA [auth E]	DA [auth E] JA [auth I] KA [auth I] TA [auth P] U [auth A] DA [auth E], JA [auth I], KA [auth I], TA [auth P], U [auth A], V [auth A]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain DA [auth E] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain TA [auth P] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain DA [auth E] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain TA [auth P] Focus chain U [auth A] Focus chain V [auth A]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain RA [auth L] SDF format, chain BA [auth D] MOL2 format, chain RA [auth L] MOL2 format, chain BA [auth D] mmCIF format, chain RA [auth L] mmCIF format, chain BA [auth D]	BA [auth D], RA [auth L]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain RA [auth L] Interactions & Density Focus chain BA [auth D] Focus chain RA [auth L]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain UA [auth Q] MOL2 format, chain UA [auth Q] mmCIF format, chain UA [auth Q]	UA [auth Q]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain UA [auth Q] Interactions & Density Focus chain UA [auth Q]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.2
MODEL REFINEMENT	Coot	0.9.8
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Foundation for Polish Science	Poland	POIR.04.04.00-00-5B54/17-00
Foundation for Polish Science	Poland	TEAM TECH CORE FACILITY/2017-4/6

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release
Version 2.0: 2026-09-02
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary

9TGG | pdb_00009tgg

Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin

Literature

High-resolution cryo-EM structures of plant cytochrome b6f at work

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)