7ZYV

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7QRM


Literature

High-resolution cryo-EM structures of plant cytochrome b 6 f 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-eadd9688

  • DOI: https://doi.org/10.1126/sciadv.add9688
  • Primary Citation of Related Structures:  
    7QRM, 7ZYV

  • 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6
A, I
215Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00165 (Spinacia oleracea)
Explore P00165 
Go to UniProtKB:  P00165
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00165
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4
B, J
160Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00166 (Spinacia oleracea)
Explore P00166 
Go to UniProtKB:  P00166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00166
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome f
C, K
320Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16013 (Spinacia oleracea)
Explore P16013 
Go to UniProtKB:  P16013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16013
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
D, L
230Spinacia oleraceaMutation(s): 0 
EC: 7.1.1.6
Membrane Entity: Yes 
UniProt
Find proteins for P08980 (Spinacia oleracea)
Explore P08980 
Go to UniProtKB:  P08980
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08980
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 6
E, M
31Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9M3L0 (Spinacia oleracea)
Explore Q9M3L0 
Go to UniProtKB:  Q9M3L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M3L0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7
F, N
131Spinacia oleraceaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5
G, O
37Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P69461 (Spinacia oleracea)
Explore P69461 
Go to UniProtKB:  P69461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69461
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8
H, P
29Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P61045 (Spinacia oleracea)
Explore P61045 
Go to UniProtKB:  P61045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61045
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Thylakoid soluble phosphoproteinQ [auth R],
R [auth Q]
103Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for Q8GT36 (Spinacia oleracea)
Explore Q8GT36 
Go to UniProtKB:  Q8GT36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GT36
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
LA [auth I],
V [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

Download Ideal Coordinates CCD File 
EA [auth D],
UA [auth L]
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

Download Ideal Coordinates CCD File 
AA [auth B]
OA [auth J]
PA [auth J]
TA [auth K]
Y [auth A]
AA [auth B],
OA [auth J],
PA [auth J],
TA [auth K],
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

Download Ideal Coordinates CCD File 
DA [auth C],
KA [auth I],
SA [auth K],
U [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
IA [auth I],
JA [auth I],
S [auth A],
T [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR (Subject of Investigation/LOI)
Query on BCR

Download Ideal Coordinates CCD File 
GA [auth F],
WA [auth P]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
UMQ (Subject of Investigation/LOI)
Query on UMQ

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
HA [auth H]
MA [auth I]
NA [auth I]
BA [auth B],
CA [auth B],
HA [auth H],
MA [auth I],
NA [auth I],
QA [auth J],
RA [auth J],
W [auth A],
X [auth A],
XA [auth P]
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
FA [auth D],
VA [auth L]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCv3.3.1

Structure Validation

View Full Validation Report



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: 2023-01-25
    Type: Initial release