9TGG | pdb_00009tgg

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


Experimental Data Snapshot

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

Starting Models: experimental
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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

  • DOI: https://doi.org/10.1126/sciadv.add9688
  • Primary Citation of 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 6 f (Cyt b 6 f) 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 6 f 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 6 f 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6
A, I
215Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P00165 (Spinacia oleracea)
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UniProt GroupP00165
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4
B, J
160Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P00166 (Spinacia oleracea)
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UniProt GroupP00166
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome f
C, K
285Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P16013 (Spinacia oleracea)
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UniProt GroupP16013
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
D, L
179Spinacia oleraceaMutation(s): 0 
EC: 7.1.1.6
UniProt
Find proteins for P08980 (Spinacia oleracea)
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UniProt GroupP08980
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 6
E, M
31Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for Q9M3L0 (Spinacia oleracea)
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UniProt GroupQ9M3L0
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7
F, N
36Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P80883 (Spinacia oleracea)
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UniProt GroupP80883
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5
G, O
37Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P69461 (Spinacia oleracea)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8
H, P
29Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P61045 (Spinacia oleracea)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Plastocyanin, chloroplastic99Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P00289 (Spinacia oleracea)
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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NA [auth J],
X [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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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
PL9 (Subject of Investigation/LOI)
Query on PL9

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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
HEC (Subject of Investigation/LOI)
Query on HEC

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AA [auth C],
IA [auth I],
PA [auth K],
T [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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GA [auth I],
HA [auth I],
R [auth A],
S [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR (Subject of Investigation/LOI)
Query on BCR

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EA [auth H],
SA [auth P]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ
Query on UMQ

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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
FES (Subject of Investigation/LOI)
Query on FES

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BA [auth D],
RA [auth L]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

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UA [auth Q]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.2
MODEL REFINEMENTCoot0.9.8
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandPOIR.04.04.00-00-5B54/17-00
Foundation for Polish SciencePolandTEAM TECH CORE FACILITY/2017-4/6

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release